| 2006-04-03 | @ SDN | 1 | L 1-6 | 0-1 | 5 | 43,767 | Jason Schmidt | Jake Peavy | Jake Peavy | Jason Schmidt | | 1 | 6 | -5 |
| 2006-04-05 | @ SDN | 2 | W 3-1 | 1-1 | 4 | 23,721 | Matt Morris | Shawn Estes | Matt Morris | Shawn Estes | Tim Worrell | 4 | 7 | -3 |
| 2006-04-06 | vs ATL | 3 | W 6-4 | 2-1 | 2 | 42,795 | Noah Lowry | Jorge Sosa | Jeff Fassero | Jorge Sosa | Tim Worrell | 10 | 11 | -1 |
| 2006-04-07 | vs ATL | 4 | L 6-14 | 2-2 | 4 | 39,737 | Matt Cain | Kyle Davies | Mike Remlinger | Tyler Walker | | 16 | 25 | -9 |
| 2006-04-08 | vs ATL | 5 | W 12-6 | 3-2 | 2 | 39,050 | Jamey Wright | Tim Hudson | Jamey Wright | Tim Hudson | | 28 | 31 | -3 |
| 2006-04-09 | vs ATL | 6 | W 6-5 | 4-2 | 2 | 37,321 | Jason Schmidt | John Smoltz | Tim Worrell | Chris Reitsma | | 34 | 36 | -2 |
| 2006-04-13 | vs HOU | 7 | W 5-3 | 5-3 | 2 | 34,267 | Matt Morris | Brandon Backe | Matt Morris | Taylor Buchholz | Tim Worrell | 39 | 39 | 0 |
| 2006-04-13 | vs HOU | 8 | L 0-8 | 5-3 | 2 | 33,034 | Matt Cain | Roy Oswalt | Roy Oswalt | Matt Cain | | 39 | 47 | -8 |
| 2006-04-14 | @ LAN | 9 | W 2-1 | 6-3 | 1 | 45,940 | Jamey Wright | Brad Penny | Jamey Wright | Hong-Chih Kuo | Tim Worrell | 41 | 48 | -7 |
| 2006-04-15 | @ LAN | 10 | L 1-3 | 6-4 | 2 | 55,132 | Jason Schmidt | Odalis Perez | Odalis Perez | Jason Schmidt | Danys Baez | 42 | 51 | -9 |
| 2006-04-16 | @ LAN | 11 | W 2-0 | 7-4 | 1 | 47,024 | Brad Hennessey | Jae Weong Seo | Brad Hennessey | Jae Weong Seo | Tim Worrell | 44 | 51 | -7 |
| 2006-04-17 | @ ARI | 12 | W 10-9 | 8-4 | 1 | 21,610 | Jeff Fassero | Miguel Batista | Steve Kline | Jose Valverde | Tim Worrell | 54 | 60 | -6 |
| 2006-04-18 | @ ARI | 13 | L 4-7 | 8-5 | 1 | 23,255 | Matt Morris | Russ Ortiz | Brandon Lyon | Matt Morris | | 58 | 67 | -9 |
| 2006-04-19 | @ ARI | 14 | L 3-10 | 8-6 | 1 | 23,083 | Matt Cain | Brandon Webb | Brandon Webb | Matt Cain | | 61 | 77 | -16 |
| 2006-04-20 | @ ARI | 15 | W 9-7 | 9-6 | 1 | 23,792 | Jamey Wright | Claudio Vargas | Tim Worrell | Brandon Medders | | 70 | 84 | -14 |
| 2006-04-21 | @ COL | 16 | L 8-9 | 9-7 | 2 | 30,339 | Jason Schmidt | Jason Jennings | David Cortes | Tim Worrell | | 78 | 93 | -15 |
| 2006-04-22 | @ COL | 17 | W 6-4 | 10-7 | 1 | 36,035 | Brad Hennessey | Aaron Cook | Brad Hennessey | Aaron Cook | Armando Benitez | 84 | 97 | -13 |
| 2006-04-23 | @ COL | 18 | L 2-3 | 10-8 | 2 | 30,310 | Matt Morris | Jeff Francis | David Cortes | Jeff Fassero | | 86 | 100 | -14 |
| 2006-04-24 | vs NYN | 19 | W 6-2 | 11-8 | 1 | 36,855 | Matt Cain | Tom Glavine | Matt Cain | Tom Glavine | | 92 | 102 | -10 |
| 2006-04-25 | vs NYN | 20 | L 1-4 | 11-9 | 2 | 35,775 | Jamey Wright | Steve Trachsel | Steve Trachsel | Jamey Wright | Billy Wagner | 93 | 106 | -13 |
| 2006-04-26 | vs NYN | 21 | L 7-9 | 11-10 | 2 | 34,454 | Matt Morris | Brian Bannister | Darren Oliver | Scott Munter | | 100 | 115 | -15 |
| 2006-04-28 | vs ARI | 22 | W 10-2 | 12-10 | 2 | 39,561 | Jason Schmidt | Miguel Batista | Jason Schmidt | Miguel Batista | | 110 | 117 | -7 |
| 2006-04-29 | vs ARI | 23 | W 3-2 | 13-10 | 2 | 38,187 | Brad Hennessey | Juan Cruz | Armando Benitez | Luis Vizcaino | | 113 | 119 | -6 |
| 2006-04-30 | vs ARI | 24 | L 2-8 | 13-11 | 2 | 38,266 | Matt Cain | Brandon Webb | Brandon Webb | Matt Cain | | 115 | 127 | -12 |
| 2006-05-01 | vs SDN | 25 | L 4-10 | 13-12 | 2 | 33,780 | Jamey Wright | Jake Peavy | Jake Peavy | Jamey Wright | | 119 | 137 | -18 |
| 2006-05-02 | vs SDN | 26 | L 3-5 | 13-13 | 3 | 34,641 | Matt Morris | Woody Williams | Woody Williams | Matt Morris | Trevor Hoffman | 122 | 142 | -20 |
| 2006-05-03 | @ MIL | 27 | W 2-0 | 14-13 | 3 | 17,358 | Jason Schmidt | David Bush | Jason Schmidt | David Bush | | 124 | 142 | -18 |
| 2006-05-04 | @ MIL | 28 | L 4-7 | 14-14 | 3 | 21,038 | Brad Hennessey | Doug Davis | Doug Davis | Brad Hennessey | Derrick Turnbow | 128 | 149 | -21 |
| 2006-05-05 | @ PHI | 29 | L 3-8 | 14-15 | 4 | 37,269 | Matt Cain | Gavin Floyd | Gavin Floyd | Matt Cain | | 131 | 157 | -26 |
| 2006-05-06 | @ PHI | 30 | L 1-4 | 14-16 | 4 | 44,042 | Jamey Wright | Ryan Madson | Ryan Madson | Jamey Wright | Tom Gordon | 132 | 161 | -29 |
| 2006-05-07 | @ PHI | 31 | L 5-9 | 14-17 | 5 | 39,315 | Matt Morris | Jon Lieber | Jon Lieber | Matt Morris | | 137 | 170 | -33 |
| 2006-05-08 | vs HOU | 32 | W 7-5 | 15-17 | 5 | 36,342 | Noah Lowry | Roy Oswalt | Noah Lowry | Roy Oswalt | Armando Benitez | 144 | 175 | -31 |
| 2006-05-09 | vs CHN | 33 | W 6-1 | 16-17 | 5 | 39,357 | Jason Schmidt | Rich Hill | Jason Schmidt | Rich Hill | | 150 | 176 | -26 |
| 2006-05-10 | vs CHN | 34 | L 1-8 | 16-18 | 5 | 39,655 | Matt Cain | Carlos Zambrano | Carlos Zambrano | Matt Cain | | 151 | 184 | -33 |
| 2006-05-11 | vs CHN | 35 | W 9-3 | 17-18 | 5 | 38,132 | Jamey Wright | Sean Marshall | Jamey Wright | Sean Marshall | | 160 | 187 | -27 |
| 2006-05-12 | vs LAN | 36 | L 1-6 | 17-19 | 5 | 42,885 | Matt Morris | Brad Penny | Brad Penny | Matt Morris | | 161 | 193 | -32 |
| 2006-05-13 | vs LAN | 37 | W 6-5 | 18-19 | 5 | 42,864 | Noah Lowry | Aaron Sele | Armando Benitez | Danys Baez | | 167 | 198 | -31 |
| 2006-05-14 | vs LAN | 38 | L 3-6 | 18-20 | 5 | 42,984 | Jason Schmidt | Jae Weong Seo | Odalis Perez | Steve Kline | Joe Beimel | 170 | 204 | -34 |
| 2006-05-15 | @ HOU | 39 | W 10-1 | 19-20 | 5 | 32,980 | Brad Hennessey | Taylor Buchholz | Brad Hennessey | Taylor Buchholz | | 180 | 205 | -25 |
| 2006-05-16 | @ HOU | 40 | W 14-3 | 20-20 | 5 | 35,286 | Jamey Wright | Wandy Rodriguez | Jamey Wright | Wandy Rodriguez | | 194 | 208 | -14 |
| 2006-05-17 | @ HOU | 41 | W 10-1 | 21-20 | 5 | 36,327 | Matt Morris | Fernando Nieve | Matt Morris | Fernando Nieve | | 204 | 209 | -5 |
| 2006-05-19 | @ OAK | 42 | L 0-1 | 21-21 | 5 | 35,077 | Noah Lowry | Dan Haren | Dan Haren | Noah Lowry | Huston Street | 204 | 210 | -6 |
| 2006-05-20 | @ OAK | 43 | W 4-2 | 22-21 | 5 | 35,077 | Jason Schmidt | Brad Halsey | Armando Benitez | Kiko Calero | | 208 | 212 | -4 |
| 2006-05-21 | @ OAK | 44 | W 6-0 | 23-21 | 5 | 35,077 | Matt Cain | Joe Blanton | Matt Cain | Joe Blanton | | 214 | 212 | 2 |
| 2006-05-22 | vs SLN | 45 | W 9-2 | 24-21 | 4 | 38,133 | Jamey Wright | Mark Mulder | Jamey Wright | Mark Mulder | | 223 | 214 | 9 |
| 2006-05-23 | vs SLN | 46 | L 5-8 | 24-22 | 5 | 37,986 | Matt Morris | Jason Marquis | Jason Marquis | Matt Morris | Jason Isringhausen | 228 | 222 | 6 |
| 2006-05-24 | vs SLN | 47 | L 4-10 | 24-23 | 5 | 37,752 | Noah Lowry | Brad Thompson | Adam Wainwright | Noah Lowry | | 232 | 232 | 0 |
| 2006-05-26 | vs COL | 48 | W 9-0 | 25-23 | 5 | 40,923 | Jason Schmidt | Jeff Francis | Jason Schmidt | Jeff Francis | | 241 | 232 | 9 |
| 2006-05-27 | vs COL | 49 | W 4-1 | 26-23 | 3 | 40,350 | Matt Cain | Josh Fogg | Matt Cain | Josh Fogg | Armando Benitez | 245 | 233 | 12 |
| 2006-05-28 | vs COL | 50 | L 3-6 | 26-24 | 5 | 42,935 | Jamey Wright | Byung-Hyun Kim | Byung-Hyun Kim | Jamey Wright | Brian Fuentes | 248 | 239 | 9 |
| 2006-05-29 | @ FLO | 51 | L 1-5 | 26-25 | 5 | 7,683 | Matt Morris | Scott Olsen | Scott Olsen | Matt Morris | | 249 | 244 | 5 |
| 2006-05-30 | @ FLO | 52 | L 3-5 | 26-26 | 5 | 10,189 | Noah Lowry | Brian Moehler | Brian Moehler | Noah Lowry | Joe Borowski | 252 | 249 | 3 |
| 2006-05-31 | @ FLO | 53 | W 6-1 | 27-26 | 5 | 8,017 | Jason Schmidt | Josh Johnson | Jason Schmidt | Josh Johnson | | 258 | 250 | 8 |
| 2006-06-03 | @ NYN | 54 | W 6-4 | 28-27 | 4 | 0 | Matt Cain | Orlando Hernandez | Matt Cain | Orlando Hernandez | Armando Benitez | 264 | 254 | 10 |
| 2006-06-03 | @ NYN | 55 | L 2-3 | 28-27 | 4 | 45,576 | Jamey Wright | Tom Glavine | Duaner Sanchez | Brian Wilson | | 266 | 257 | 9 |
| 2006-06-04 | @ NYN | 56 | W 7-6 | 29-27 | 4 | 48,791 | Matt Morris | Steve Trachsel | Jonathan Sanchez | Pedro Feliciano | Jeremy Accardo | 273 | 263 | 10 |
| 2006-06-05 | vs FLO | 57 | W 14-2 | 30-27 | 4 | 35,438 | Noah Lowry | Brian Moehler | Noah Lowry | Brian Moehler | Brad Hennessey | 287 | 265 | 22 |
| 2006-06-06 | vs FLO | 58 | W 2-1 | 31-27 | 3 | 33,987 | Jason Schmidt | Josh Johnson | Jason Schmidt | Josh Johnson | | 289 | 266 | 23 |
| 2006-06-07 | vs FLO | 59 | L 1-8 | 31-28 | 4 | 35,740 | Jamey Wright | Dontrelle Willis | Dontrelle Willis | Jamey Wright | | 290 | 274 | 16 |
| 2006-06-08 | vs PIT | 60 | W 5-4 | 32-28 | 3 | 34,540 | Matt Cain | Zach Duke | Armando Benitez | Damaso Marte | | 295 | 278 | 17 |
| 2006-06-09 | vs PIT | 61 | L 2-3 | 32-29 | 4 | 38,766 | Matt Morris | Victor Santos | Victor Santos | Matt Morris | Mike Gonzalez | 297 | 281 | 16 |
| 2006-06-10 | vs PIT | 62 | L 0-2 | 32-30 | 4 | 37,302 | Noah Lowry | Ian Snell | Ian Snell | Noah Lowry | Mike Gonzalez | 297 | 283 | 14 |
| 2006-06-11 | vs PIT | 63 | L 5-7 | 32-31 | 4 | 39,850 | Jason Schmidt | Paul Maholm | Matt Capps | Tim Worrell | Mike Gonzalez | 302 | 290 | 12 |
| 2006-06-13 | @ ARI | 64 | L 1-2 | 32-32 | 5 | 25,595 | Jamey Wright | Enrique Gonzalez | Enrique Gonzalez | Jamey Wright | Jorge Julio | 303 | 292 | 11 |
| 2006-06-14 | @ ARI | 65 | W 11-4 | 33-32 | 5 | 24,820 | Matt Cain | Claudio Vargas | Matt Cain | Claudio Vargas | | 314 | 296 | 18 |
| 2006-06-15 | @ ARI | 66 | W 8-2 | 34-32 | 5 | 21,559 | Matt Morris | Miguel Batista | Matt Morris | Miguel Batista | | 322 | 298 | 24 |
| 2006-06-16 | @ SEA | 67 | L 4-5 | 34-33 | 5 | 41,133 | Noah Lowry | Felix Hernandez | Felix Hernandez | Noah Lowry | J.J. Putz | 326 | 303 | 23 |
| 2006-06-17 | @ SEA | 68 | L 1-8 | 34-34 | 5 | 45,229 | Jason Schmidt | Gil Meche | Gil Meche | Jason Schmidt | | 327 | 311 | 16 |
| 2006-06-18 | @ SEA | 69 | L 1-5 | 34-35 | 5 | 45,216 | Jamey Wright | Jamie Moyer | Jamie Moyer | Jamey Wright | | 328 | 316 | 12 |
| 2006-06-19 | vs ANA | 70 | W 2-1 | 35-35 | 5 | 37,594 | Matt Cain | Kelvim Escobar | Matt Cain | Kelvim Escobar | Armando Benitez | 330 | 317 | 13 |
| 2006-06-20 | vs ANA | 71 | W 3-2 | 36-35 | 5 | 40,887 | Matt Morris | John Lackey | Matt Morris | John Lackey | Armando Benitez | 333 | 319 | 14 |
| 2006-06-21 | vs ANA | 72 | L 3-6 | 36-36 | 5 | 40,900 | Noah Lowry | Jeff Weaver | Scot Shields | Jeremy Accardo | Francisco Rodriguez | 336 | 325 | 11 |
| 2006-06-23 | vs OAK | 73 | L 3-4 | 36-37 | 4 | 42,948 | Jason Schmidt | Joe Blanton | Kiko Calero | Armando Benitez | Huston Street | 339 | 329 | 10 |
| 2006-06-24 | vs OAK | 74 | W 8-7 | 37-37 | 4 | 42,866 | Jamey Wright | Dan Haren | Tim Worrell | Huston Street | | 347 | 336 | 11 |
| 2006-06-25 | vs OAK | 75 | L 4-10 | 37-38 | 4 | 42,414 | Matt Cain | Esteban Loaiza | Esteban Loaiza | Matt Cain | | 351 | 346 | 5 |
| 2006-06-27 | vs TEX | 76 | W 5-3 | 38-38 | 4 | 36,053 | Matt Morris | Kevin Millwood | Matt Morris | Kevin Millwood | Jeremy Accardo | 356 | 349 | 7 |
| 2006-06-28 | vs TEX | 77 | W 5-1 | 39-38 | 4 | 37,275 | Noah Lowry | John Rheinecker | Noah Lowry | John Rheinecker | | 361 | 350 | 11 |
| 2006-06-29 | vs TEX | 78 | W 2-1 | 40-38 | 4 | 38,212 | Jason Schmidt | John Koronka | Jonathan Sanchez | Scott Feldman | Jeremy Accardo | 363 | 351 | 12 |
| 2006-06-30 | @ SDN | 79 | L 5-6 | 40-39 | 4 | 39,511 | Jamey Wright | Chan Ho Park | Brian Sikorski | Jeremy Accardo | | 368 | 357 | 11 |
| 2006-07-01 | @ SDN | 80 | L 4-7 | 41-40 | 4 | 23,888 | Matt Cain | Mike Thompson | Jon Adkins | Brian Wilson | Trevor Hoffman | 372 | 364 | 8 |
| 2006-07-01 | @ SDN | 81 | W 4-1 | 41-40 | 4 | 43,029 | Brad Hennessey | Woody Williams | Steve Kline | Alan Embree | Armando Benitez | 376 | 365 | 11 |
| 2006-07-02 | @ SDN | 82 | W 6-2 | 42-40 | 3 | 39,837 | Matt Morris | Chris Young | Matt Morris | Chris Young | Brian Wilson | 382 | 367 | 15 |
| 2006-07-03 | @ COL | 83 | W 9-6 | 43-40 | 2 | 48,364 | Noah Lowry | Aaron Cook | Jeremy Accardo | Ramon Ramirez | Armando Benitez | 391 | 373 | 18 |
| 2006-07-04 | @ COL | 84 | L 1-6 | 43-41 | 4 | 48,078 | Jason Schmidt | Jeff Francis | Jeff Francis | Jason Schmidt | | 392 | 379 | 13 |
| 2006-07-05 | @ COL | 85 | L 3-5 | 43-42 | 4 | 23,485 | Jamey Wright | Josh Fogg | Josh Fogg | Jamey Wright | Brian Fuentes | 395 | 384 | 11 |
| 2006-07-06 | @ LAN | 86 | W 5-4 | 44-42 | 4 | 42,515 | Matt Cain | Mark Hendrickson | Brad Hennessey | Mark Hendrickson | Armando Benitez | 400 | 388 | 12 |
| 2006-07-07 | @ LAN | 87 | L 7-9 | 44-43 | 4 | 53,991 | Matt Morris | Chad Billingsley | Danys Baez | Jeremy Accardo | Takashi Saito | 407 | 397 | 10 |
| 2006-07-08 | @ LAN | 88 | W 11-7 | 45-43 | 4 | 46,496 | Noah Lowry | Derek Lowe | Noah Lowry | Derek Lowe | Armando Benitez | 418 | 404 | 14 |
| 2006-07-09 | @ LAN | 89 | L 1-3 | 45-44 | 4 | 41,849 | Jason Schmidt | Aaron Sele | Aaron Sele | Jason Schmidt | Takashi Saito | 419 | 407 | 12 |
| 2006-07-14 | vs PHI | 90 | W 5-3 | 46-44 | 3 | 38,009 | Matt Morris | Jon Lieber | Matt Morris | Jon Lieber | Armando Benitez | 424 | 410 | 14 |
| 2006-07-15 | vs PHI | 91 | L 6-14 | 46-45 | 3 | 41,401 | Noah Lowry | Cory Lidle | Cory Lidle | Noah Lowry | | 430 | 424 | 6 |
| 2006-07-16 | vs PHI | 92 | L 2-6 | 46-46 | 3 | 38,241 | Matt Cain | Brett Myers | Brett Myers | Steve Kline | | 432 | 430 | 2 |
| 2006-07-17 | vs MIL | 93 | L 1-10 | 46-47 | 4 | 36,738 | Jason Schmidt | Zach Jackson | Zach Jackson | Jason Schmidt | | 433 | 440 | -7 |
| 2006-07-18 | vs MIL | 94 | W 4-3 | 47-47 | 3 | 37,054 | Jamey Wright | Tomo Ohka | Jamey Wright | Geremi Gonzalez | Armando Benitez | 437 | 443 | -6 |
| 2006-07-19 | vs MIL | 95 | W 7-6 | 48-47 | 2 | 39,570 | Matt Morris | Doug Davis | Brian Wilson | Derrick Turnbow | | 444 | 449 | -5 |
| 2006-07-20 | vs SDN | 96 | W 9-3 | 49-47 | 2 | 42,047 | Noah Lowry | Chan Ho Park | Noah Lowry | Chan Ho Park | | 453 | 452 | 1 |
| 2006-07-21 | vs SDN | 97 | W 8-2 | 50-47 | 2 | 42,683 | Matt Cain | Jake Peavy | Matt Cain | Jake Peavy | | 461 | 454 | 7 |
| 2006-07-22 | vs SDN | 98 | W 4-3 | 51-47 | 1 | 42,955 | Jason Schmidt | Woody Williams | Jason Schmidt | Woody Williams | Armando Benitez | 465 | 457 | 8 |
| 2006-07-23 | vs SDN | 99 | L 5-6 | 51-48 | 2 | 41,209 | Jamey Wright | Clay Hensley | Jon Adkins | Brian Wilson | Trevor Hoffman | 470 | 463 | 7 |
| 2006-07-25 | @ WAS | 100 | L 6-8 | 51-49 | 3 | 33,358 | Matt Morris | Ramon Ortiz | Ramon Ortiz | Matt Morris | Chad Cordero | 476 | 471 | 5 |
| 2006-07-26 | @ WAS | 101 | L 3-4 | 51-50 | 3 | 30,248 | Noah Lowry | Pedro Astacio | Saul Rivera | Armando Benitez | | 479 | 475 | 4 |
| 2006-07-27 | @ WAS | 102 | L 5-6 | 51-51 | 3 | 29,717 | Matt Cain | Livan Hernandez | Livan Hernandez | Matt Cain | Chad Cordero | 484 | 481 | 3 |
| 2006-07-28 | @ PIT | 103 | L 0-3 | 51-52 | 3 | 38,092 | Jason Schmidt | Kip Wells | Kip Wells | Jason Schmidt | Mike Gonzalez | 484 | 484 | 0 |
| 2006-07-29 | @ PIT | 104 | L 3-4 | 51-53 | 3 | 38,373 | Jamey Wright | Tom Gorzelanny | Tom Gorzelanny | Jamey Wright | Mike Gonzalez | 487 | 488 | -1 |
| 2006-07-30 | @ PIT | 105 | L 1-2 | 51-54 | 3 | 26,516 | Matt Morris | Zach Duke | John Grabow | Steve Kline | | 488 | 490 | -2 |
| 2006-07-31 | vs WAS | 106 | L 7-10 | 51-55 | 4 | 37,106 | Noah Lowry | Pedro Astacio | Pedro Astacio | Noah Lowry | Chad Cordero | 495 | 500 | -5 |
| 2006-08-01 | vs WAS | 107 | L 1-4 | 51-56 | 5 | 37,258 | Matt Cain | Livan Hernandez | Livan Hernandez | Matt Cain | Chad Cordero | 496 | 504 | -8 |
| 2006-08-02 | vs WAS | 108 | W 8-6 | 52-56 | 5 | 38,283 | Jason Schmidt | Tony Armas | Jason Schmidt | Tony Armas | Mike Stanton | 504 | 510 | -6 |
| 2006-08-04 | vs COL | 109 | L 2-5 | 52-57 | 5 | 38,033 | Matt Morris | Jeff Francis | Jeff Francis | Matt Morris | Brian Fuentes | 506 | 515 | -9 |
| 2006-08-05 | vs COL | 110 | L 1-2 | 52-58 | 5 | 39,014 | Noah Lowry | Jason Jennings | Jeremy Affeldt | Brad Hennessey | Brian Fuentes | 507 | 517 | -10 |
| 2006-08-06 | vs COL | 111 | W 6-2 | 53-58 | 5 | 39,288 | Matt Cain | Aaron Cook | Matt Cain | Aaron Cook | | 513 | 519 | -6 |
| 2006-08-07 | @ ARI | 112 | W 8-4 | 54-58 | 5 | 25,531 | Jason Schmidt | Enrique Gonzalez | Jason Schmidt | Jeff Bajenaru | | 521 | 523 | -2 |
| 2006-08-08 | @ ARI | 113 | L 1-5 | 54-59 | 5 | 35,146 | Jamey Wright | Juan Cruz | Juan Cruz | Jamey Wright | | 522 | 528 | -6 |
| 2006-08-09 | @ ARI | 114 | L 3-5 | 54-60 | 5 | 23,782 | Matt Morris | Miguel Batista | Miguel Batista | Matt Morris | Jorge Julio | 525 | 533 | -8 |
| 2006-08-11 | @ LAN | 115 | L 2-3 | 54-61 | 5 | 53,695 | Noah Lowry | Mark Hendrickson | Brett Tomko | Mike Stanton | Jonathan Broxton | 527 | 536 | -9 |
| 2006-08-12 | @ LAN | 116 | L 5-6 | 54-62 | 5 | 46,444 | Matt Cain | Brad Penny | Brad Penny | Matt Cain | Takashi Saito | 532 | 542 | -10 |
| 2006-08-13 | @ LAN | 117 | L 0-1 | 54-63 | 5 | 55,699 | Jason Schmidt | Greg Maddux | Takashi Saito | Vinnie Chulk | | 532 | 543 | -11 |
| 2006-08-14 | @ SDN | 118 | W 1-0 | 55-63 | 5 | 31,774 | Brad Hennessey | Clay Hensley | Brad Hennessey | Clay Hensley | Armando Benitez | 533 | 543 | -10 |
| 2006-08-15 | @ SDN | 119 | W 3-2 | 56-63 | 5 | 31,601 | Matt Morris | Chris Young | Mike Stanton | Scott Linebrink | Armando Benitez | 536 | 545 | -9 |
| 2006-08-16 | @ SDN | 120 | W 7-5 | 57-63 | 5 | 33,938 | Noah Lowry | Chan Ho Park | Steve Kline | Alan Embree | Mike Stanton | 543 | 550 | -7 |
| 2006-08-17 | @ SDN | 121 | W 8-4 | 58-63 | 5 | 29,734 | Matt Cain | Jake Peavy | Matt Cain | Jake Peavy | | 551 | 554 | -3 |
| 2006-08-18 | vs LAN | 122 | W 7-3 | 59-63 | 5 | 42,862 | Jason Schmidt | Brad Penny | Jason Schmidt | Brad Penny | | 558 | 557 | 1 |
| 2006-08-19 | vs LAN | 123 | L 7-14 | 59-64 | 5 | 42,833 | Brad Hennessey | Greg Maddux | Greg Maddux | Brad Hennessey | | 565 | 571 | -6 |
| 2006-08-20 | vs LAN | 124 | L 2-5 | 59-65 | 5 | 42,052 | Matt Morris | Derek Lowe | Derek Lowe | Matt Morris | Takashi Saito | 567 | 576 | -9 |
| 2006-08-21 | vs ARI | 125 | W 5-0 | 60-65 | 4 | 38,203 | Noah Lowry | Livan Hernandez | Noah Lowry | Livan Hernandez | | 572 | 576 | -4 |
| 2006-08-22 | vs ARI | 126 | W 7-6 | 61-65 | 4 | 37,242 | Matt Cain | Brandon Webb | Mike Stanton | Tony Pena | Steve Kline | 579 | 582 | -3 |
| 2006-08-23 | vs ARI | 127 | W 7-6 | 62-65 | 4 | 38,831 | Jason Schmidt | Enrique Gonzalez | Steve Kline | Brandon Lyon | Armando Benitez | 586 | 588 | -2 |
| 2006-08-24 | vs CIN | 128 | L 3-6 | 62-66 | 4 | 38,754 | Brad Hennessey | Eric Milton | Ryan Franklin | Vinnie Chulk | David Weathers | 589 | 594 | -5 |
| 2006-08-25 | vs CIN | 129 | W 4-1 | 63-66 | 4 | 37,801 | Matt Morris | Aaron Harang | Matt Morris | Aaron Harang | | 593 | 595 | -2 |
| 2006-08-26 | vs CIN | 130 | W 4-1 | 64-66 | 3 | 41,362 | Noah Lowry | Bronson Arroyo | Noah Lowry | Bronson Arroyo | Mike Stanton | 597 | 596 | 1 |
| 2006-08-27 | vs CIN | 131 | W 8-0 | 65-66 | 3 | 39,097 | Matt Cain | Kyle Lohse | Matt Cain | Kyle Lohse | | 605 | 596 | 9 |
| 2006-08-29 | @ ATL | 132 | L 8-13 | 65-67 | 3 | 23,756 | Jason Schmidt | Tim Hudson | Tim Hudson | Jason Schmidt | | 613 | 609 | 4 |
| 2006-08-30 | @ ATL | 133 | L 3-5 | 65-68 | 3 | 24,952 | Brad Hennessey | Chuck James | Chuck James | Brad Hennessey | Bob Wickman | 616 | 614 | 2 |
| 2006-08-31 | @ ATL | 134 | W 8-6 | 66-68 | 3 | 24,748 | Matt Morris | John Smoltz | Matt Morris | John Smoltz | Armando Benitez | 624 | 620 | 4 |
| 2006-09-01 | @ CHN | 135 | L 2-6 | 66-69 | 3 | 38,582 | Noah Lowry | Rich Hill | Rich Hill | Noah Lowry | | 626 | 626 | 0 |
| 2006-09-02 | @ CHN | 136 | W 4-2 | 67-69 | 3 | 40,135 | Matt Cain | Sean Marshall | Matt Cain | Sean Marshall | Mike Stanton | 630 | 628 | 2 |
| 2006-09-03 | @ CHN | 137 | W 7-4 | 68-69 | 3 | 40,702 | Jason Schmidt | Angel Guzman | Jason Schmidt | Michael Wuertz | Mike Stanton | 637 | 632 | 5 |
| 2006-09-04 | @ CIN | 138 | W 5-4 | 69-69 | 3 | 25,515 | Brad Hennessey | Aaron Harang | Kevin Correia | David Weathers | Mike Stanton | 642 | 636 | 6 |
| 2006-09-05 | @ CIN | 139 | L 0-3 | 69-70 | 3 | 20,751 | Matt Morris | Bronson Arroyo | Bronson Arroyo | Matt Morris | | 642 | 639 | 3 |
| 2006-09-06 | @ CIN | 140 | W 3-2 | 70-70 | 3 | 20,571 | Jonathan Sanchez | Sun-Woo Kim | Jonathan Sanchez | Sun-Woo Kim | Mike Stanton | 645 | 641 | 4 |
| 2006-09-08 | vs SDN | 141 | W 4-0 | 71-70 | 3 | 38,988 | Matt Cain | Jake Peavy | Matt Cain | Jake Peavy | | 649 | 641 | 8 |
| 2006-09-09 | vs SDN | 142 | W 5-4 | 72-70 | 3 | 38,680 | Jason Schmidt | David Wells | Mike Stanton | Rudy Seanez | | 654 | 645 | 9 |
| 2006-09-10 | vs SDN | 143 | L 2-10 | 72-71 | 3 | 36,757 | Matt Morris | Woody Williams | Woody Williams | Matt Morris | | 656 | 655 | 1 |
| 2006-09-12 | vs COL | 144 | W 10-6 | 73-71 | 3 | 33,416 | Jonathan Sanchez | Denny Bautista | Kevin Correia | Denny Bautista | | 666 | 661 | 5 |
| 2006-09-13 | vs COL | 145 | L 8-9 | 73-72 | 3 | 34,847 | Noah Lowry | Jason Jennings | Jason Jennings | Noah Lowry | Brian Fuentes | 674 | 670 | 4 |
| 2006-09-14 | vs COL | 146 | W 5-0 | 74-72 | 3 | 35,167 | Matt Cain | Aaron Cook | Matt Cain | Aaron Cook | | 679 | 670 | 9 |
| 2006-09-15 | @ SLN | 147 | L 4-14 | 74-73 | 3 | 45,927 | Brad Hennessey | Jeff Suppan | Jeff Suppan | Brad Hennessey | | 683 | 684 | -1 |
| 2006-09-16 | @ SLN | 148 | L 1-6 | 74-74 | 3 | 45,445 | Matt Morris | Chris Carpenter | Chris Carpenter | Matt Morris | | 684 | 690 | -6 |
| 2006-09-18 | @ COL | 149 | L 8-20 | 74-75 | 3 | 18,346 | Noah Lowry | Justin Hampson | Justin Hampson | Noah Lowry | | 692 | 710 | -18 |
| 2006-09-19 | @ COL | 150 | L 4-12 | 74-76 | 3 | 20,373 | Matt Cain | Jason Jennings | Jason Jennings | Matt Cain | Jeremy Affeldt | 696 | 722 | -26 |
| 2006-09-20 | @ COL | 151 | W 7-4 | 75-76 | 3 | 19,324 | Jason Schmidt | Aaron Cook | Brian Wilson | Manuel Corpas | Mike Stanton | 703 | 726 | -23 |
| 2006-09-21 | @ MIL | 152 | L 4-9 | 75-77 | 3 | 28,719 | Matt Morris | David Bush | David Bush | Matt Morris | | 707 | 735 | -28 |
| 2006-09-22 | @ MIL | 153 | L 12-13 | 75-78 | 3 | 21,796 | Jonathan Sanchez | Doug Davis | Jose Capellan | Vinnie Chulk | Francisco Cordero | 719 | 748 | -29 |
| 2006-09-23 | @ MIL | 154 | L 8-10 | 75-79 | 3 | 33,989 | Noah Lowry | Chris Capuano | Jose Capellan | Jack Taschner | Francisco Cordero | 727 | 758 | -31 |
| 2006-09-24 | @ MIL | 155 | L 3-5 | 75-80 | 3 | 23,049 | Matt Cain | Ben Sheets | Ben Sheets | Matt Cain | Francisco Cordero | 730 | 763 | -33 |
| 2006-09-25 | vs ARI | 156 | L 1-7 | 75-81 | 3 | 33,919 | Jason Schmidt | Edgar Gonzalez | Edgar Gonzalez | Jason Schmidt | | 731 | 770 | -39 |
| 2006-09-26 | vs ARI | 157 | W 4-2 | 76-81 | 3 | 35,121 | Matt Morris | Brandon Webb | Mike Stanton | Randy Choate | | 735 | 772 | -37 |
| 2006-09-27 | vs ARI | 158 | L 3-6 | 76-82 | 3 | 34,503 | Jonathan Sanchez | Claudio Vargas | Claudio Vargas | Jonathan Sanchez | Jose Valverde | 738 | 778 | -40 |
| 2006-09-29 | vs LAN | 159 | L 3-4 | 76-83 | 3 | 42,587 | Noah Lowry | Hong-Chih Kuo | Jonathan Broxton | Mike Stanton | Takashi Saito | 741 | 782 | -41 |
| 2006-09-30 | vs LAN | 160 | L 2-4 | 76-84 | 3 | 42,769 | Matt Cain | Greg Maddux | Greg Maddux | Matt Cain | Takashi Saito | 743 | 786 | -43 |
| 2006-10-01 | vs LAN | 161 | L 3-4 | 76-85 | 3 | 42,831 | Jason Schmidt | Eric Stults | Chad Billingsley | Brad Hennessey | Joe Beimel | 746 | 790 | -44 |