| 2006-04-03 | @ COL | 1 | L 2-3 | 0-1 | 3 | 47,278 | Brandon Webb | Jason Jennings | Mike DeJean | Jason Grimsley | | 2 | 3 | -1 |
| 2006-04-05 | @ COL | 2 | W 4-2 | 1-1 | 1 | 18,553 | Orlando Hernandez | Aaron Cook | Orlando Hernandez | Aaron Cook | Jose Valverde | 6 | 5 | 1 |
| 2006-04-06 | @ COL | 3 | W 12-5 | 2-1 | 1 | 18,406 | Miguel Batista | Jeff Francis | Miguel Batista | Jeff Francis | | 18 | 10 | 8 |
| 2006-04-07 | @ MIL | 4 | L 1-3 | 2-2 | 1 | 25,737 | Russ Ortiz | David Bush | David Bush | Russ Ortiz | Derrick Turnbow | 19 | 13 | 6 |
| 2006-04-08 | @ MIL | 5 | L 4-5 | 2-3 | 4 | 29,226 | Brandon Webb | Doug Davis | Danny Kolb | Luis Vizcaino | | 23 | 18 | 5 |
| 2006-04-09 | @ MIL | 6 | W 7-0 | 3-3 | 3 | 28,115 | Claudio Vargas | Chris Capuano | Claudio Vargas | Chris Capuano | | 30 | 18 | 12 |
| 2006-04-11 | vs COL | 7 | L 5-6 | 3-4 | 4 | 37,355 | Orlando Hernandez | Aaron Cook | Aaron Cook | Orlando Hernandez | Brian Fuentes | 35 | 24 | 11 |
| 2006-04-12 | vs COL | 8 | W 5-4 | 4-4 | 3 | 18,664 | Miguel Batista | Jeff Francis | Greg Aquino | Ray King | Jose Valverde | 40 | 28 | 12 |
| 2006-04-13 | vs COL | 9 | L 3-5 | 4-5 | 4 | 18,745 | Russ Ortiz | Josh Fogg | Josh Fogg | Russ Ortiz | Brian Fuentes | 43 | 33 | 10 |
| 2006-04-14 | vs HOU | 10 | W 5-1 | 5-5 | 3 | 24,512 | Brandon Webb | Andy Pettitte | Brandon Webb | Andy Pettitte | | 48 | 34 | 14 |
| 2006-04-15 | vs HOU | 11 | L 0-10 | 5-6 | 4 | 25,042 | Claudio Vargas | Wandy Rodriguez | Wandy Rodriguez | Claudio Vargas | | 48 | 44 | 4 |
| 2006-04-16 | vs HOU | 12 | L 5-8 | 5-7 | 4 | 21,191 | Orlando Hernandez | Fernando Nieve | Russ Springer | Orlando Hernandez | Brad Lidge | 53 | 52 | 1 |
| 2006-04-17 | vs SFN | 13 | L 9-10 | 5-8 | 5 | 21,610 | Miguel Batista | Jeff Fassero | Steve Kline | Jose Valverde | Tim Worrell | 62 | 62 | 0 |
| 2006-04-18 | vs SFN | 14 | W 7-4 | 6-8 | 4 | 23,255 | Russ Ortiz | Matt Morris | Brandon Lyon | Matt Morris | | 69 | 66 | 3 |
| 2006-04-19 | vs SFN | 15 | W 10-3 | 7-8 | 3 | 23,083 | Brandon Webb | Matt Cain | Brandon Webb | Matt Cain | | 79 | 69 | 10 |
| 2006-04-20 | vs SFN | 16 | L 7-9 | 7-9 | 3 | 23,792 | Claudio Vargas | Jamey Wright | Tim Worrell | Brandon Medders | | 86 | 78 | 8 |
| 2006-04-21 | @ LAN | 17 | L 3-6 | 7-10 | 5 | 44,294 | Orlando Hernandez | Odalis Perez | Odalis Perez | Orlando Hernandez | Danys Baez | 89 | 84 | 5 |
| 2006-04-22 | @ LAN | 18 | W 5-4 | 8-10 | 3 | 51,878 | Miguel Batista | Jae Weong Seo | Miguel Batista | Jae Weong Seo | Jose Valverde | 94 | 88 | 6 |
| 2006-04-23 | @ LAN | 19 | L 4-6 | 8-11 | 5 | 48,394 | Russ Ortiz | Brett Tomko | Brett Tomko | Russ Ortiz | Danys Baez | 98 | 94 | 4 |
| 2006-04-24 | @ SDN | 20 | W 4-1 | 9-11 | 4 | 19,718 | Brandon Webb | Chan Ho Park | Brandon Webb | Chan Ho Park | Jose Valverde | 102 | 95 | 7 |
| 2006-04-25 | @ SDN | 21 | W 7-0 | 10-11 | 3 | 21,281 | Claudio Vargas | Jake Peavy | Claudio Vargas | Jake Peavy | | 109 | 95 | 14 |
| 2006-04-26 | @ SDN | 22 | W 3-2 | 11-11 | 3 | 22,247 | Orlando Hernandez | Woody Williams | Orlando Hernandez | Woody Williams | Jose Valverde | 112 | 97 | 15 |
| 2006-04-28 | @ SFN | 23 | L 2-10 | 11-12 | 3 | 39,561 | Miguel Batista | Jason Schmidt | Jason Schmidt | Miguel Batista | | 114 | 107 | 7 |
| 2006-04-29 | @ SFN | 24 | L 2-3 | 11-13 | 4 | 38,187 | Juan Cruz | Brad Hennessey | Armando Benitez | Luis Vizcaino | | 116 | 110 | 6 |
| 2006-04-30 | @ SFN | 25 | W 8-2 | 12-13 | 3 | 38,266 | Brandon Webb | Matt Cain | Brandon Webb | Matt Cain | | 124 | 112 | 12 |
| 2006-05-01 | vs LAN | 26 | W 3-2 | 13-13 | 3 | 20,099 | Claudio Vargas | Brad Penny | Claudio Vargas | Brad Penny | Jose Valverde | 127 | 114 | 13 |
| 2006-05-02 | vs LAN | 27 | W 10-8 | 14-13 | 2 | 23,198 | Orlando Hernandez | Odalis Perez | Luis Vizcaino | Takashi Saito | Jose Valverde | 137 | 122 | 15 |
| 2006-05-03 | vs CHN | 28 | W 5-1 | 15-13 | 2 | 25,331 | Miguel Batista | Greg Maddux | Miguel Batista | Greg Maddux | Jose Valverde | 142 | 123 | 19 |
| 2006-05-04 | vs CHN | 29 | W 6-0 | 16-13 | 1 | 24,552 | Juan Cruz | Rich Hill | Juan Cruz | Rich Hill | | 148 | 123 | 25 |
| 2006-05-05 | vs CIN | 30 | W 7-1 | 17-13 | 1 | 21,072 | Brandon Webb | Elizardo Ramirez | Brandon Webb | Elizardo Ramirez | | 155 | 124 | 31 |
| 2006-05-06 | vs CIN | 31 | W 3-1 | 18-13 | 1 | 27,398 | Claudio Vargas | Bronson Arroyo | Claudio Vargas | Bronson Arroyo | Jose Valverde | 158 | 125 | 33 |
| 2006-05-07 | vs CIN | 32 | L 8-9 | 18-14 | 2 | 27,707 | Orlando Hernandez | David Williams | David Williams | Orlando Hernandez | David Weathers | 166 | 134 | 32 |
| 2006-05-09 | @ PIT | 33 | L 0-3 | 18-15 | 2 | 16,961 | Miguel Batista | Ian Snell | Ian Snell | Miguel Batista | Mike Gonzalez | 166 | 137 | 29 |
| 2006-05-10 | @ PIT | 34 | W 7-4 | 19-15 | 2 | 14,509 | Brandon Webb | Paul Maholm | Brandon Webb | Damaso Marte | Jose Valverde | 173 | 141 | 32 |
| 2006-05-12 | @ SLN | 35 | L 3-5 | 19-16 | 3 | 41,085 | Juan Cruz | Mark Mulder | Mark Mulder | Juan Cruz | Jason Isringhausen | 176 | 146 | 30 |
| 2006-05-13 | @ SLN | 36 | L 1-9 | 19-17 | 3 | 40,585 | Claudio Vargas | Jason Marquis | Jason Marquis | Claudio Vargas | | 177 | 155 | 22 |
| 2006-05-14 | @ SLN | 37 | W 7-6 | 20-17 | 3 | 40,891 | Miguel Batista | Chris Carpenter | Luis Vizcaino | Adam Wainwright | Jose Valverde | 184 | 161 | 23 |
| 2006-05-15 | vs SDN | 38 | W 6-5 | 21-17 | 2 | 19,838 | Brandon Webb | Chan Ho Park | Jose Valverde | Scott Cassidy | | 190 | 166 | 24 |
| 2006-05-16 | vs SDN | 39 | W 5-2 | 22-17 | 1 | 20,015 | Orlando Hernandez | Jake Peavy | Jason Grimsley | Jake Peavy | Jose Valverde | 195 | 168 | 27 |
| 2006-05-17 | vs SDN | 40 | L 10-14 | 22-18 | 2 | 18,012 | Juan Cruz | Mike Thompson | Mike Thompson | Juan Cruz | | 205 | 182 | 23 |
| 2006-05-19 | vs ATL | 41 | W 10-9 | 23-18 | 1 | 25,056 | Miguel Batista | John Thomson | Jose Valverde | Chris Reitsma | | 215 | 191 | 24 |
| 2006-05-20 | vs ATL | 42 | W 13-0 | 24-18 | 1 | 35,382 | Brandon Webb | Travis Smith | Brandon Webb | Travis Smith | | 228 | 191 | 37 |
| 2006-05-21 | vs ATL | 43 | L 1-2 | 24-19 | 2 | 33,102 | Juan Cruz | Tim Hudson | Tim Hudson | Juan Cruz | Macay McBride | 229 | 193 | 36 |
| 2006-05-22 | vs PIT | 44 | W 4-3 | 25-19 | 1 | 18,103 | Orlando Hernandez | Oliver Perez | Brandon Medders | Damaso Marte | Jose Valverde | 233 | 196 | 37 |
| 2006-05-23 | vs PIT | 45 | W 7-3 | 26-19 | 1 | 19,993 | Claudio Vargas | Victor Santos | Claudio Vargas | Victor Santos | | 240 | 199 | 41 |
| 2006-05-24 | vs PIT | 46 | W 8-7 | 27-19 | 1 | 18,394 | Miguel Batista | Zach Duke | Miguel Batista | Zach Duke | Jose Valverde | 248 | 206 | 42 |
| 2006-05-26 | @ CIN | 47 | W 3-0 | 28-19 | 1 | 33,751 | Brandon Webb | Eric Milton | Brandon Webb | Eric Milton | | 251 | 206 | 45 |
| 2006-05-27 | @ CIN | 48 | W 7-0 | 29-19 | 1 | 36,884 | Juan Cruz | Aaron Harang | Juan Cruz | Aaron Harang | | 258 | 206 | 52 |
| 2006-05-28 | @ CIN | 49 | L 4-5 | 29-20 | 1 | 27,694 | Enrique Gonzalez | Bronson Arroyo | David Weathers | Jose Valverde | | 262 | 211 | 51 |
| 2006-05-29 | @ NYN | 50 | L 7-8 | 29-21 | 1 | 39,826 | Claudio Vargas | Steve Trachsel | Duaner Sanchez | Jose Valverde | | 269 | 219 | 50 |
| 2006-05-30 | @ NYN | 51 | W 7-2 | 30-21 | 1 | 35,448 | Miguel Batista | Alay Soler | Miguel Batista | Alay Soler | | 276 | 221 | 55 |
| 2006-05-31 | @ NYN | 52 | L 0-1 | 30-22 | 1 | 37,735 | Brandon Webb | Pedro Martinez | Duaner Sanchez | Jason Grimsley | | 276 | 222 | 54 |
| 2006-06-01 | @ ATL | 53 | W 2-1 | 31-22 | 1 | 23,376 | Juan Cruz | Horacio Ramirez | Juan Cruz | Horacio Ramirez | Jorge Julio | 278 | 223 | 55 |
| 2006-06-03 | @ ATL | 54 | W 4-2 | 33-22 | 1 | 27,126 | Enrique Gonzalez | John Smoltz | Enrique Gonzalez | John Smoltz | Jorge Julio | 282 | 225 | 57 |
| 2006-06-03 | @ ATL | 55 | W 13-9 | 33-22 | 1 | 40,212 | Claudio Vargas | John Thomson | Claudio Vargas | John Thomson | | 295 | 234 | 61 |
| 2006-06-04 | @ ATL | 56 | W 9-3 | 34-22 | 1 | 29,141 | Miguel Batista | Jorge Sosa | Miguel Batista | Jorge Sosa | | 304 | 237 | 67 |
| 2006-06-05 | vs PHI | 57 | L 3-4 | 34-23 | 1 | 20,644 | Brandon Webb | Cory Lidle | Aaron Fultz | Brandon Lyon | Tom Gordon | 307 | 241 | 66 |
| 2006-06-06 | vs PHI | 58 | L 1-10 | 34-24 | 1 | 22,661 | Russ Ortiz | Cole Hamels | Cole Hamels | Russ Ortiz | | 308 | 251 | 57 |
| 2006-06-07 | vs PHI | 59 | L 3-7 | 34-25 | 1 | 21,031 | Dustin Nippert | Ryan Madson | Ryan Madson | Dustin Nippert | | 311 | 258 | 53 |
| 2006-06-08 | vs NYN | 60 | L 1-7 | 34-26 | 1 | 20,845 | Claudio Vargas | Orlando Hernandez | Orlando Hernandez | Claudio Vargas | | 312 | 265 | 47 |
| 2006-06-09 | vs NYN | 61 | L 6-10 | 34-27 | 1 | 23,671 | Miguel Batista | Steve Trachsel | Steve Trachsel | Miguel Batista | | 318 | 275 | 43 |
| 2006-06-10 | vs NYN | 62 | L 0-5 | 34-28 | 1 | 33,671 | Brandon Webb | Alay Soler | Alay Soler | Brandon Webb | | 318 | 280 | 38 |
| 2006-06-11 | vs NYN | 63 | L 2-15 | 34-29 | 2 | 28,475 | Russ Ortiz | Pedro Martinez | Pedro Martinez | Russ Ortiz | | 320 | 295 | 25 |
| 2006-06-13 | vs SFN | 64 | W 2-1 | 35-29 | 1 | 25,595 | Enrique Gonzalez | Jamey Wright | Enrique Gonzalez | Jamey Wright | Jorge Julio | 322 | 296 | 26 |
| 2006-06-14 | vs SFN | 65 | L 4-11 | 35-30 | 1 | 24,820 | Claudio Vargas | Matt Cain | Matt Cain | Claudio Vargas | | 326 | 307 | 19 |
| 2006-06-15 | vs SFN | 66 | L 2-8 | 35-31 | 2 | 21,559 | Miguel Batista | Matt Morris | Matt Morris | Miguel Batista | | 328 | 315 | 13 |
| 2006-06-16 | @ TEX | 67 | L 3-5 | 35-32 | 2 | 28,167 | Brandon Webb | Kevin Millwood | Kevin Millwood | Brandon Webb | Akinori Otsuka | 331 | 320 | 11 |
| 2006-06-17 | @ TEX | 68 | L 4-8 | 35-33 | 2 | 41,165 | Kevin Jarvis | John Koronka | John Koronka | Kevin Jarvis | | 335 | 328 | 7 |
| 2006-06-18 | @ TEX | 69 | L 7-10 | 35-34 | 3 | 24,358 | Enrique Gonzalez | Kameron Loe | Francisco Cordero | Luis Vizcaino | Akinori Otsuka | 342 | 338 | 4 |
| 2006-06-19 | @ PIT | 70 | W 5-4 | 36-34 | 3 | 15,032 | Claudio Vargas | Zach Duke | Greg Aquino | Salomon Torres | Jorge Julio | 347 | 342 | 5 |
| 2006-06-20 | @ TBA | 71 | L 5-8 | 36-35 | 3 | 10,430 | Miguel Batista | Mark Hendrickson | Mark Hendrickson | Miguel Batista | | 352 | 350 | 2 |
| 2006-06-21 | @ TBA | 72 | L 2-3 | 36-36 | 3 | 17,182 | Brandon Webb | James Shields | James Shields | Brandon Webb | Brian Meadows | 354 | 353 | 1 |
| 2006-06-22 | @ TBA | 73 | L 1-4 | 36-37 | 5 | 17,888 | Edgar Gonzalez | Scott Kazmir | Scott Kazmir | Edgar Gonzalez | Brian Meadows | 355 | 357 | -2 |
| 2006-06-23 | vs ANA | 74 | L 2-8 | 36-38 | 5 | 23,684 | Enrique Gonzalez | Ervin Santana | Ervin Santana | Enrique Gonzalez | | 357 | 365 | -8 |
| 2006-06-24 | vs ANA | 75 | L 4-6 | 36-39 | 5 | 33,525 | Claudio Vargas | Bartolo Colon | Brendan Donnelly | Brandon Medders | Francisco Rodriguez | 361 | 371 | -10 |
| 2006-06-25 | vs ANA | 76 | W 9-7 | 37-39 | 5 | 24,778 | Miguel Batista | Kelvim Escobar | Miguel Batista | Kelvim Escobar | Jorge Julio | 370 | 378 | -8 |
| 2006-06-27 | vs SEA | 77 | L 7-11 | 37-40 | 5 | 25,061 | Brandon Webb | Jarrod Washburn | Jake Woods | Brandon Lyon | J.J. Putz | 377 | 389 | -12 |
| 2006-06-28 | vs SEA | 78 | L 3-10 | 37-41 | 5 | 19,706 | Edgar Gonzalez | Felix Hernandez | Felix Hernandez | Edgar Gonzalez | | 380 | 399 | -19 |
| 2006-06-29 | vs SEA | 79 | L 2-3 | 37-42 | 5 | 20,564 | Enrique Gonzalez | Gil Meche | Eddie Guardado | Jorge Julio | J.J. Putz | 382 | 402 | -20 |
| 2006-06-30 | @ OAK | 80 | W 6-4 | 38-42 | 5 | 16,756 | Claudio Vargas | Kirk Saarloos | Claudio Vargas | Brad Halsey | Jorge Julio | 388 | 406 | -18 |
| 2006-07-01 | @ OAK | 81 | W 7-2 | 39-42 | 5 | 19,024 | Miguel Batista | Esteban Loaiza | Miguel Batista | Esteban Loaiza | | 395 | 408 | -13 |
| 2006-07-02 | @ OAK | 82 | W 3-1 | 40-42 | 5 | 19,130 | Brandon Webb | Barry Zito | Brandon Webb | Barry Zito | | 398 | 409 | -11 |
| 2006-07-03 | @ LAN | 83 | L 4-10 | 40-43 | 5 | 47,698 | Juan Cruz | Derek Lowe | Derek Lowe | Juan Cruz | | 402 | 419 | -17 |
| 2006-07-04 | @ LAN | 84 | L 3-11 | 40-44 | 5 | 55,816 | Enrique Gonzalez | Aaron Sele | Aaron Sele | Enrique Gonzalez | | 405 | 430 | -25 |
| 2006-07-05 | @ LAN | 85 | L 4-5 | 40-45 | 5 | 38,505 | Claudio Vargas | Brad Penny | Brad Penny | Claudio Vargas | Takashi Saito | 409 | 435 | -26 |
| 2006-07-07 | @ COL | 86 | W 4-3 | 41-45 | 5 | 26,313 | Miguel Batista | Byung-Hyun Kim | Brandon Medders | Byung-Hyun Kim | Jorge Julio | 413 | 438 | -25 |
| 2006-07-08 | @ COL | 87 | W 8-7 | 42-45 | 5 | 22,874 | Brandon Webb | Jason Jennings | Luis Vizcaino | Brian Fuentes | Jorge Julio | 421 | 445 | -24 |
| 2006-07-09 | @ COL | 88 | W 8-5 | 43-45 | 5 | 22,210 | Juan Cruz | Aaron Cook | Edgar Gonzalez | Scott Dohmann | Jorge Julio | 429 | 450 | -21 |
| 2006-07-14 | vs MIL | 89 | W 4-3 | 44-45 | 4 | 24,117 | Miguel Batista | Doug Davis | Brandon Medders | Derrick Turnbow | | 433 | 453 | -20 |
| 2006-07-15 | vs MIL | 90 | W 8-1 | 45-45 | 4 | 26,318 | Brandon Webb | Chris Capuano | Brandon Webb | Chris Capuano | | 441 | 454 | -13 |
| 2006-07-16 | vs MIL | 91 | L 5-10 | 45-46 | 4 | 29,303 | Claudio Vargas | David Bush | David Bush | Claudio Vargas | | 446 | 464 | -18 |
| 2006-07-17 | vs LAN | 92 | W 8-3 | 46-46 | 2 | 23,518 | Enrique Gonzalez | Aaron Sele | Enrique Gonzalez | Aaron Sele | | 454 | 467 | -13 |
| 2006-07-18 | vs LAN | 93 | L 1-4 | 46-47 | 4 | 27,471 | Juan Cruz | Chad Billingsley | Chad Billingsley | Juan Cruz | | 455 | 471 | -16 |
| 2006-07-19 | vs LAN | 94 | W 8-0 | 47-47 | 3 | 23,583 | Miguel Batista | Derek Lowe | Miguel Batista | Derek Lowe | | 463 | 471 | -8 |
| 2006-07-20 | vs LAN | 95 | W 5-2 | 48-47 | 3 | 25,294 | Brandon Webb | Mark Hendrickson | Brandon Webb | Mark Hendrickson | Jorge Julio | 468 | 473 | -5 |
| 2006-07-21 | vs COL | 96 | W 6-2 | 49-47 | 3 | 23,068 | Claudio Vargas | Aaron Cook | Claudio Vargas | Aaron Cook | | 474 | 475 | -1 |
| 2006-07-22 | vs COL | 97 | W 4-3 | 50-47 | 2 | 28,745 | Enrique Gonzalez | Josh Fogg | Brandon Medders | Jose Mesa | Jorge Julio | 478 | 478 | 0 |
| 2006-07-23 | vs COL | 98 | L 7-9 | 50-48 | 3 | 29,310 | Juan Cruz | Byung-Hyun Kim | Tom Martin | Jorge Julio | Brian Fuentes | 485 | 487 | -2 |
| 2006-07-25 | @ PHI | 99 | W 6-5 | 51-48 | 2 | 24,499 | Miguel Batista | Ryan Madson | Tony Pena | Ryan Franklin | | 491 | 492 | -1 |
| 2006-07-26 | @ PHI | 100 | L 4-6 | 51-49 | 2 | 45,459 | Brandon Webb | Jon Lieber | Jon Lieber | Brandon Webb | Tom Gordon | 495 | 498 | -3 |
| 2006-07-27 | @ PHI | 101 | L 2-5 | 51-50 | 2 | 31,752 | Claudio Vargas | Cory Lidle | Cory Lidle | Claudio Vargas | Tom Gordon | 497 | 503 | -6 |
| 2006-07-28 | @ HOU | 102 | W 8-7 | 52-50 | 2 | 43,201 | Enrique Gonzalez | Brandon Backe | Tony Pena | Andy Pettitte | | 505 | 510 | -5 |
| 2006-07-29 | @ HOU | 103 | L 1-4 | 52-51 | 2 | 43,386 | Juan Cruz | Roy Oswalt | Roy Oswalt | Juan Cruz | Brad Lidge | 506 | 514 | -8 |
| 2006-07-30 | @ HOU | 104 | W 7-6 | 53-51 | 2 | 41,867 | Miguel Batista | Roger Clemens | Tony Pena | Trever Miller | Jorge Julio | 513 | 520 | -7 |
| 2006-07-31 | @ CHN | 105 | W 15-4 | 54-51 | 2 | 39,226 | Brandon Webb | Mark Prior | Brandon Webb | Mark Prior | | 528 | 524 | 4 |
| 2006-08-01 | @ CHN | 106 | L 3-9 | 54-52 | 2 | 38,970 | Claudio Vargas | Rich Hill | Rich Hill | Claudio Vargas | | 531 | 533 | -2 |
| 2006-08-03 | @ CHN | 107 | W 10-2 | 55-53 | 2 | 0 | Juan Cruz | Carlos Marmol | Juan Cruz | Carlos Marmol | | 541 | 535 | 6 |
| 2006-08-03 | @ CHN | 108 | L 3-7 | 55-53 | 2 | 40,715 | Enrique Gonzalez | Juan Mateo | Juan Mateo | Enrique Gonzalez | | 544 | 542 | 2 |
| 2006-08-04 | vs HOU | 109 | L 7-8 | 55-54 | 2 | 24,485 | Miguel Batista | Roy Oswalt | Trever Miller | Tony Pena | Dan Wheeler | 551 | 550 | 1 |
| 2006-08-05 | vs HOU | 110 | L 3-9 | 55-55 | 2 | 33,069 | Dustin Nippert | Roger Clemens | Roger Clemens | Dustin Nippert | | 554 | 559 | -5 |
| 2006-08-06 | vs HOU | 111 | W 4-3 | 56-55 | 2 | 25,999 | Claudio Vargas | Andy Pettitte | Claudio Vargas | Andy Pettitte | Jorge Julio | 558 | 562 | -4 |
| 2006-08-07 | vs SFN | 112 | L 4-8 | 56-56 | 3 | 25,531 | Enrique Gonzalez | Jason Schmidt | Jason Schmidt | Jeff Bajenaru | | 562 | 570 | -8 |
| 2006-08-08 | vs SFN | 113 | W 5-1 | 57-56 | 3 | 35,146 | Juan Cruz | Jamey Wright | Juan Cruz | Jamey Wright | | 567 | 571 | -4 |
| 2006-08-09 | vs SFN | 114 | W 5-3 | 58-56 | 2 | 23,782 | Miguel Batista | Matt Morris | Miguel Batista | Matt Morris | Jorge Julio | 572 | 574 | -2 |
| 2006-08-11 | vs FLO | 115 | L 1-4 | 58-57 | 2 | 21,950 | Livan Hernandez | Josh Johnson | Josh Johnson | Livan Hernandez | Joe Borowski | 573 | 578 | -5 |
| 2006-08-12 | vs FLO | 116 | W 6-3 | 59-57 | 2 | 25,168 | Brandon Webb | Scott Olsen | Brandon Webb | Scott Olsen | Jorge Julio | 579 | 581 | -2 |
| 2006-08-13 | vs FLO | 117 | L 5-6 | 59-58 | 3 | 30,974 | Enrique Gonzalez | Ricky Nolasco | Ricky Nolasco | Enrique Gonzalez | Joe Borowski | 584 | 587 | -3 |
| 2006-08-14 | @ COL | 118 | L 3-4 | 59-59 | 3 | 21,365 | Claudio Vargas | Jeff Francis | Jeremy Affeldt | Tony Pena | | 587 | 591 | -4 |
| 2006-08-15 | @ COL | 119 | W 2-1 | 60-59 | 2 | 22,076 | Miguel Batista | Jason Jennings | Brandon Medders | Ramon Ramirez | | 589 | 592 | -3 |
| 2006-08-16 | @ COL | 120 | W 9-5 | 61-59 | 2 | 23,415 | Livan Hernandez | Aaron Cook | Livan Hernandez | Aaron Cook | | 598 | 597 | 1 |
| 2006-08-17 | @ COL | 121 | L 4-8 | 61-60 | 2 | 23,390 | Brandon Webb | Josh Fogg | Josh Fogg | Brandon Webb | | 602 | 605 | -3 |
| 2006-08-18 | @ SDN | 122 | L 2-8 | 61-61 | 2 | 35,196 | Enrique Gonzalez | Woody Williams | Woody Williams | Enrique Gonzalez | | 604 | 613 | -9 |
| 2006-08-19 | @ SDN | 123 | W 5-3 | 62-61 | 2 | 34,250 | Claudio Vargas | Mike Thompson | Claudio Vargas | Mike Thompson | Tony Pena | 609 | 616 | -7 |
| 2006-08-20 | @ SDN | 124 | L 1-2 | 62-62 | 2 | 34,843 | Miguel Batista | Chris Young | Cla Meredith | Brandon Medders | | 610 | 618 | -8 |
| 2006-08-21 | @ SFN | 125 | L 0-5 | 62-63 | 3 | 38,203 | Livan Hernandez | Noah Lowry | Noah Lowry | Livan Hernandez | | 610 | 623 | -13 |
| 2006-08-22 | @ SFN | 126 | L 6-7 | 62-64 | 3 | 37,242 | Brandon Webb | Matt Cain | Mike Stanton | Tony Pena | Steve Kline | 616 | 630 | -14 |
| 2006-08-23 | @ SFN | 127 | L 6-7 | 62-65 | 3 | 38,831 | Enrique Gonzalez | Jason Schmidt | Steve Kline | Brandon Lyon | Armando Benitez | 622 | 637 | -15 |
| 2006-08-25 | vs LAN | 128 | W 9-7 | 63-65 | 3 | 26,276 | Claudio Vargas | Greg Maddux | Brandon Lyon | Aaron Sele | | 631 | 644 | -13 |
| 2006-08-26 | vs LAN | 129 | L 3-4 | 63-66 | 4 | 40,358 | Miguel Batista | Derek Lowe | Jonathan Broxton | Luis Vizcaino | Takashi Saito | 634 | 648 | -14 |
| 2006-08-27 | vs LAN | 130 | L 3-6 | 63-67 | 4 | 30,337 | Livan Hernandez | Chad Billingsley | Chad Billingsley | Livan Hernandez | Takashi Saito | 637 | 654 | -17 |
| 2006-08-28 | vs SDN | 131 | W 7-4 | 64-67 | 4 | 29,269 | Brandon Webb | Woody Williams | Brandon Webb | Woody Williams | | 644 | 658 | -14 |
| 2006-08-29 | vs SDN | 132 | L 3-8 | 64-68 | 4 | 21,551 | Enrique Gonzalez | Chris Young | Chris Young | Enrique Gonzalez | | 647 | 666 | -19 |
| 2006-08-30 | vs SDN | 133 | L 1-4 | 64-69 | 4 | 20,223 | Claudio Vargas | Mike Thompson | Mike Thompson | Claudio Vargas | Trevor Hoffman | 648 | 670 | -22 |
| 2006-09-02 | @ WAS | 134 | L 6-7 | 64-71 | 4 | 22,012 | Miguel Batista | Billy Traber | Chad Cordero | Brandon Lyon | | 654 | 677 | -23 |
| 2006-09-02 | @ WAS | 135 | L 3-4 | 64-71 | 4 | 22,922 | Livan Hernandez | Jason Bergmann | Saul Rivera | Livan Hernandez | Chad Cordero | 657 | 681 | -24 |
| 2006-09-03 | @ WAS | 136 | L 3-5 | 64-72 | 4 | 30,771 | Brandon Webb | Tony Armas | Ryan Wagner | Brandon Webb | Jon Rauch | 660 | 686 | -26 |
| 2006-09-04 | @ FLO | 137 | L 5-8 | 64-73 | 4 | 12,191 | Enrique Gonzalez | Brian Moehler | Randy Messenger | Enrique Gonzalez | Joe Borowski | 665 | 694 | -29 |
| 2006-09-05 | @ FLO | 138 | W 4-0 | 65-73 | 4 | 13,236 | Claudio Vargas | Dontrelle Willis | Claudio Vargas | Dontrelle Willis | | 669 | 694 | -25 |
| 2006-09-06 | @ FLO | 139 | L 0-2 | 65-74 | 4 | 12,561 | Edgar Gonzalez | Anibal Sanchez | Anibal Sanchez | Edgar Gonzalez | | 669 | 696 | -27 |
| 2006-09-07 | vs SLN | 140 | L 2-6 | 65-75 | 4 | 29,998 | Miguel Batista | Jeff Weaver | Jeff Weaver | Miguel Batista | | 671 | 702 | -31 |
| 2006-09-08 | vs SLN | 141 | W 13-1 | 66-75 | 4 | 25,299 | Livan Hernandez | Anthony Reyes | Livan Hernandez | Anthony Reyes | | 684 | 703 | -19 |
| 2006-09-09 | vs SLN | 142 | W 3-0 | 67-75 | 4 | 33,619 | Brandon Webb | Jason Marquis | Brandon Webb | Jason Marquis | | 687 | 703 | -16 |
| 2006-09-10 | vs SLN | 143 | W 9-7 | 68-75 | 4 | 25,381 | Enrique Gonzalez | Jeff Suppan | Luis Vizcaino | Jorge Sosa | Jose Valverde | 696 | 710 | -14 |
| 2006-09-11 | vs WAS | 144 | L 6-7 | 68-76 | 4 | 29,610 | Claudio Vargas | Billy Traber | Jon Rauch | Luis Vizcaino | Chad Cordero | 702 | 717 | -15 |
| 2006-09-12 | vs WAS | 145 | L 4-5 | 68-77 | 4 | 31,182 | Miguel Batista | Jason Bergmann | Felix Rodriguez | Tony Pena | Chad Cordero | 706 | 722 | -16 |
| 2006-09-13 | vs WAS | 146 | W 4-2 | 69-77 | 4 | 19,031 | Livan Hernandez | Tony Armas | Livan Hernandez | Tony Armas | Jose Valverde | 710 | 724 | -14 |
| 2006-09-15 | vs COL | 147 | W 5-1 | 70-77 | 4 | 22,017 | Brandon Webb | Byung-Hyun Kim | Brandon Webb | Byung-Hyun Kim | | 715 | 725 | -10 |
| 2006-09-16 | vs COL | 148 | W 7-6 | 71-77 | 4 | 27,822 | Claudio Vargas | Josh Fogg | Jorge Julio | Jeremy Affeldt | | 722 | 731 | -9 |
| 2006-09-17 | vs COL | 149 | L 1-6 | 71-78 | 4 | 28,056 | Miguel Batista | Jeff Francis | Jeff Francis | Miguel Batista | | 723 | 737 | -14 |
| 2006-09-19 | @ SDN | 150 | L 2-5 | 71-79 | 4 | 29,067 | Livan Hernandez | Clay Hensley | Clay Hensley | Livan Hernandez | Trevor Hoffman | 725 | 742 | -17 |
| 2006-09-20 | @ SDN | 151 | W 8-2 | 72-79 | 4 | 34,129 | Edgar Gonzalez | David Wells | Edgar Gonzalez | David Wells | | 733 | 744 | -11 |
| 2006-09-21 | @ SDN | 152 | L 1-3 | 72-80 | 4 | 34,238 | Brandon Webb | Woody Williams | Woody Williams | Brandon Webb | Trevor Hoffman | 734 | 747 | -13 |
| 2006-09-22 | @ LAN | 153 | L 0-2 | 72-81 | 4 | 43,990 | Claudio Vargas | Derek Lowe | Derek Lowe | Claudio Vargas | Takashi Saito | 734 | 749 | -15 |
| 2006-09-23 | @ LAN | 154 | W 9-3 | 73-81 | 4 | 49,791 | Miguel Batista | Brad Penny | Miguel Batista | Brad Penny | | 743 | 752 | -9 |
| 2006-09-24 | @ LAN | 155 | L 1-5 | 73-82 | 5 | 49,822 | Livan Hernandez | Hong-Chih Kuo | Takashi Saito | Luis Vizcaino | | 744 | 757 | -13 |
| 2006-09-25 | @ SFN | 156 | W 7-1 | 74-82 | 4 | 33,919 | Edgar Gonzalez | Jason Schmidt | Edgar Gonzalez | Jason Schmidt | | 751 | 758 | -7 |
| 2006-09-26 | @ SFN | 157 | L 2-4 | 74-83 | 4 | 35,121 | Brandon Webb | Matt Morris | Mike Stanton | Randy Choate | | 753 | 762 | -9 |
| 2006-09-27 | @ SFN | 158 | W 6-3 | 75-83 | 4 | 34,503 | Claudio Vargas | Jonathan Sanchez | Claudio Vargas | Jonathan Sanchez | Jose Valverde | 759 | 765 | -6 |
| 2006-09-28 | vs SDN | 159 | L 4-12 | 75-84 | 4 | 26,689 | Miguel Batista | Jake Peavy | Jake Peavy | Miguel Batista | | 763 | 777 | -14 |
| 2006-09-29 | vs SDN | 160 | W 3-1 | 76-84 | 4 | 30,700 | Livan Hernandez | Clay Hensley | Livan Hernandez | Clay Hensley | Jose Valverde | 766 | 778 | -12 |
| 2006-09-30 | vs SDN | 161 | L 1-3 | 76-85 | 4 | 33,019 | Juan Cruz | David Wells | David Wells | Edgar Gonzalez | Trevor Hoffman | 767 | 781 | -14 |
| 2006-10-01 | vs SDN | 162 | L 6-7 | 76-86 | 4 | 48,946 | Brandon Webb | Woody Williams | Woody Williams | Brandon Webb | Trevor Hoffman | 773 | 788 | -15 |