| 2006-04-03 | @ NYN | 1 | L 2-3 | 0-1 | 5 | 54,371 | Livan Hernandez | Tom Glavine | Tom Glavine | Livan Hernandez | Billy Wagner | 2 | 3 | -1 |
| 2006-04-05 | @ NYN | 2 | W 9-5 | 1-1 | 3 | 19,557 | John Patterson | Brian Bannister | Chad Cordero | Jorge Julio | | 11 | 8 | 3 |
| 2006-04-06 | @ NYN | 3 | L 5-10 | 1-2 | 4 | 25,839 | Ramon Ortiz | Pedro Martinez | Pedro Martinez | Ramon Ortiz | | 16 | 18 | -2 |
| 2006-04-07 | @ HOU | 4 | L 1-6 | 1-3 | 4 | 26,978 | Tony Armas | Brandon Backe | Brandon Backe | Tony Armas | | 17 | 24 | -7 |
| 2006-04-08 | @ HOU | 5 | W 12-8 | 2-3 | 3 | 39,324 | Livan Hernandez | Roy Oswalt | Livan Hernandez | Chad Qualls | | 29 | 32 | -3 |
| 2006-04-09 | @ HOU | 6 | L 3-7 | 2-4 | 3 | 31,662 | Ryan Drese | Andy Pettitte | Andy Pettitte | Ryan Drese | | 32 | 39 | -7 |
| 2006-04-10 | @ HOU | 7 | L 4-5 | 2-5 | 3 | 27,944 | John Patterson | Wandy Rodriguez | Chad Qualls | Mike Stanton | | 36 | 44 | -8 |
| 2006-04-11 | vs NYN | 8 | L 1-7 | 2-6 | 3 | 40,530 | Ramon Ortiz | Brian Bannister | Brian Bannister | Ramon Ortiz | | 37 | 51 | -14 |
| 2006-04-12 | vs NYN | 9 | L 1-3 | 2-7 | 4 | 29,985 | Tony Armas | Pedro Martinez | Pedro Martinez | Tony Armas | Billy Wagner | 38 | 54 | -16 |
| 2006-04-13 | vs NYN | 10 | L 4-13 | 2-8 | 5 | 25,465 | Livan Hernandez | Victor Zambrano | Victor Zambrano | Livan Hernandez | | 42 | 67 | -25 |
| 2006-04-14 | @ FLO | 11 | L 3-5 | 2-9 | 5 | 12,913 | Ryan Drese | Dontrelle Willis | Dontrelle Willis | Ryan Drese | Joe Borowski | 45 | 72 | -27 |
| 2006-04-15 | @ FLO | 12 | W 2-1 | 3-9 | 5 | 15,668 | John Patterson | Scott Olsen | John Patterson | Scott Olsen | Chad Cordero | 47 | 73 | -26 |
| 2006-04-16 | @ FLO | 13 | W 7-5 | 4-9 | 4 | 10,296 | Ramon Ortiz | Sergio Mitre | Gary Majewski | Matt Herges | Chad Cordero | 54 | 78 | -24 |
| 2006-04-18 | @ PHI | 14 | W 10-3 | 5-9 | 4 | 20,072 | Tony Armas | Cory Lidle | Tony Armas | Cory Lidle | | 64 | 81 | -17 |
| 2006-04-19 | @ PHI | 15 | L 6-7 | 5-10 | 4 | 27,913 | Livan Hernandez | Gavin Floyd | Ryan Franklin | Mike Stanton | | 70 | 88 | -18 |
| 2006-04-20 | @ PHI | 16 | W 10-4 | 6-10 | 4 | 28,177 | Billy Traber | Ryan Madson | Billy Traber | Ryan Madson | | 80 | 92 | -12 |
| 2006-04-21 | vs ATL | 17 | W 7-3 | 7-10 | 3 | 24,597 | John Patterson | John Smoltz | Mike Stanton | Lance Cormier | | 87 | 95 | -8 |
| 2006-04-23 | vs ATL | 18 | L 1-3 | 7-11 | 4 | 21,569 | Tony Armas | John Thomson | Lance Cormier | Gary Majewski | Mike Remlinger | 88 | 98 | -10 |
| 2006-04-24 | vs CIN | 19 | L 2-4 | 7-12 | 4 | 19,264 | Livan Hernandez | Elizardo Ramirez | Elizardo Ramirez | Livan Hernandez | David Weathers | 90 | 102 | -12 |
| 2006-04-25 | vs CIN | 20 | L 5-6 | 7-13 | 4 | 21,642 | Billy Traber | David Williams | David Williams | Billy Traber | David Weathers | 95 | 108 | -13 |
| 2006-04-26 | vs CIN | 21 | L 0-5 | 7-14 | 4 | 19,380 | Ramon Ortiz | Bronson Arroyo | Bronson Arroyo | Ramon Ortiz | | 95 | 113 | -18 |
| 2006-04-27 | @ SLN | 22 | L 2-6 | 7-15 | 4 | 39,515 | Mike O'Connor | Sidney Ponson | Sidney Ponson | Mike O'Connor | | 97 | 119 | -22 |
| 2006-04-28 | @ SLN | 23 | W 8-3 | 8-15 | 4 | 40,841 | Tony Armas | Jason Marquis | Tony Armas | Jason Marquis | | 105 | 122 | -17 |
| 2006-04-29 | @ SLN | 24 | L 1-2 | 8-16 | 4 | 39,596 | Livan Hernandez | Chris Carpenter | Braden Looper | Jon Rauch | Jason Isringhausen | 106 | 124 | -18 |
| 2006-04-30 | @ SLN | 25 | L 2-9 | 8-17 | 4 | 39,383 | Zach Day | Jeff Suppan | Jeff Suppan | Zach Day | | 108 | 133 | -25 |
| 2006-05-01 | @ NYN | 26 | L 1-2 | 8-18 | 4 | 28,310 | Ramon Ortiz | Victor Zambrano | Billy Wagner | Gary Majewski | | 109 | 135 | -26 |
| 2006-05-02 | @ NYN | 27 | W 6-2 | 9-18 | 4 | 34,046 | Mike O'Connor | John Maine | Mike O'Connor | John Maine | | 115 | 137 | -22 |
| 2006-05-03 | vs FLO | 28 | L 5-6 | 9-19 | 4 | 21,918 | Tony Armas | Brian Moehler | Ricky Nolasco | Mike Stanton | Joe Borowski | 120 | 143 | -23 |
| 2006-05-04 | vs FLO | 29 | L 3-11 | 9-20 | 4 | 20,984 | Livan Hernandez | Josh Johnson | Josh Johnson | Livan Hernandez | | 123 | 154 | -31 |
| 2006-05-05 | vs PIT | 30 | W 6-0 | 10-20 | 4 | 21,059 | Zach Day | Oliver Perez | Zach Day | Oliver Perez | | 129 | 154 | -25 |
| 2006-05-06 | vs PIT | 31 | L 4-5 | 10-21 | 4 | 29,953 | Ramon Ortiz | Victor Santos | Mike Gonzalez | Felix Rodriguez | | 133 | 159 | -26 |
| 2006-05-07 | vs PIT | 32 | W 5-4 | 11-21 | 4 | 30,659 | Mike O'Connor | Zach Duke | Mike O'Connor | Zach Duke | Chad Cordero | 138 | 163 | -25 |
| 2006-05-09 | @ CIN | 33 | W 7-1 | 12-21 | 4 | 16,716 | Tony Armas | Brandon Claussen | Tony Armas | Brandon Claussen | | 145 | 164 | -19 |
| 2006-05-10 | @ CIN | 34 | L 6-9 | 12-22 | 4 | 14,180 | Livan Hernandez | Aaron Harang | David Weathers | Mike Stanton | | 151 | 173 | -22 |
| 2006-05-11 | @ CIN | 35 | L 4-5 | 12-23 | 4 | 15,771 | Zach Day | Bronson Arroyo | Brian Shackelford | Joey Eischen | | 155 | 178 | -23 |
| 2006-05-12 | @ ATL | 36 | L 2-6 | 12-24 | 4 | 31,818 | Ramon Ortiz | John Smoltz | John Smoltz | Ramon Ortiz | | 157 | 184 | -27 |
| 2006-05-13 | @ ATL | 37 | L 5-8 | 12-25 | 4 | 37,040 | Mike O'Connor | Jorge Sosa | Chris Reitsma | Chad Cordero | | 162 | 192 | -30 |
| 2006-05-14 | @ ATL | 38 | W 8-1 | 13-25 | 4 | 31,062 | Tony Armas | John Thomson | Tony Armas | John Thomson | | 170 | 193 | -23 |
| 2006-05-16 | @ CHN | 39 | L 0-4 | 13-26 | 4 | 39,298 | Livan Hernandez | Carlos Zambrano | Carlos Zambrano | Livan Hernandez | | 170 | 197 | -27 |
| 2006-05-17 | @ CHN | 40 | L 0-5 | 13-27 | 4 | 39,757 | Zach Day | Sean Marshall | Sean Marshall | Zach Day | | 170 | 202 | -32 |
| 2006-05-18 | @ CHN | 41 | W 5-3 | 14-27 | 4 | 40,517 | Ramon Ortiz | Kerry Wood | Ramon Ortiz | Kerry Wood | Chad Cordero | 175 | 205 | -30 |
| 2006-05-19 | vs BAL | 42 | L 1-5 | 14-28 | 4 | 30,320 | Mike O'Connor | Kris Benson | Kris Benson | Mike O'Connor | | 176 | 210 | -34 |
| 2006-05-20 | vs BAL | 43 | W 8-3 | 15-28 | 4 | 32,502 | Tony Armas | Rodrigo Lopez | Jon Rauch | Rodrigo Lopez | | 184 | 213 | -29 |
| 2006-05-21 | vs BAL | 44 | W 3-1 | 16-28 | 4 | 32,152 | Livan Hernandez | Bruce Chen | Livan Hernandez | Bruce Chen | Chad Cordero | 187 | 214 | -27 |
| 2006-05-22 | vs HOU | 45 | L 3-10 | 16-29 | 4 | 18,803 | Zach Day | Wandy Rodriguez | Wandy Rodriguez | Zach Day | | 190 | 224 | -34 |
| 2006-05-23 | vs HOU | 46 | W 4-1 | 17-29 | 4 | 23,189 | Ramon Ortiz | Fernando Nieve | Ramon Ortiz | Fernando Nieve | Chad Cordero | 194 | 225 | -31 |
| 2006-05-24 | vs HOU | 47 | W 5-1 | 18-29 | 4 | 24,194 | Mike O'Connor | Roy Oswalt | Gary Majewski | Dan Wheeler | | 199 | 226 | -27 |
| 2006-05-25 | vs HOU | 48 | W 8-5 | 19-29 | 4 | 24,733 | Tony Armas | Andy Pettitte | Tony Armas | Andy Pettitte | Chad Cordero | 207 | 231 | -24 |
| 2006-05-26 | vs LAN | 49 | W 10-4 | 20-29 | 4 | 22,712 | Livan Hernandez | Brett Tomko | Livan Hernandez | Brett Tomko | | 217 | 235 | -18 |
| 2006-05-27 | vs LAN | 50 | L 1-3 | 20-30 | 4 | 26,867 | Shawn Hill | Derek Lowe | Derek Lowe | Mike Stanton | Takashi Saito | 218 | 238 | -20 |
| 2006-05-28 | vs LAN | 51 | W 10-4 | 21-30 | 4 | 30,348 | Ramon Ortiz | Jae Weong Seo | Ramon Ortiz | Jae Weong Seo | | 228 | 242 | -14 |
| 2006-05-29 | @ PHI | 52 | L 2-11 | 21-31 | 4 | 33,682 | Mike O'Connor | Jon Lieber | Clay Condrey | Mike O'Connor | | 230 | 253 | -23 |
| 2006-05-30 | @ PHI | 53 | L 2-4 | 21-32 | 4 | 23,805 | Tony Armas | Brett Myers | Brett Myers | Tony Armas | Tom Gordon | 232 | 257 | -25 |
| 2006-05-31 | @ PHI | 54 | W 3-2 | 22-32 | 4 | 30,386 | Livan Hernandez | Cory Lidle | Livan Hernandez | Cory Lidle | Chad Cordero | 235 | 259 | -24 |
| 2006-06-02 | @ MIL | 55 | W 10-4 | 23-32 | 4 | 21,476 | Ramon Ortiz | Dana Eveland | Ramon Ortiz | Dana Eveland | | 245 | 263 | -18 |
| 2006-06-03 | @ MIL | 56 | W 4-3 | 24-32 | 4 | 40,392 | Mike O'Connor | Doug Davis | Bill Bray | Derrick Turnbow | Chad Cordero | 249 | 266 | -17 |
| 2006-06-04 | @ MIL | 57 | W 8-4 | 25-32 | 4 | 21,608 | Tony Armas | Jorge de la Rosa | Tony Armas | Jorge de la Rosa | | 257 | 270 | -13 |
| 2006-06-05 | @ ATL | 58 | W 5-4 | 26-32 | 4 | 20,702 | Livan Hernandez | Tim Hudson | Livan Hernandez | Tim Hudson | Chad Cordero | 262 | 274 | -12 |
| 2006-06-06 | @ ATL | 59 | L 3-5 | 26-33 | 4 | 23,497 | Shawn Hill | Horacio Ramirez | Horacio Ramirez | Shawn Hill | Ken Ray | 265 | 279 | -14 |
| 2006-06-07 | @ ATL | 60 | W 5-2 | 27-33 | 4 | 32,001 | Ramon Ortiz | John Smoltz | Ramon Ortiz | John Smoltz | Chad Cordero | 270 | 281 | -11 |
| 2006-06-08 | vs PHI | 61 | W 5-2 | 28-33 | 4 | 24,669 | Mike O'Connor | Eude Brito | Mike O'Connor | Eude Brito | Chad Cordero | 275 | 283 | -8 |
| 2006-06-09 | vs PHI | 62 | W 9-8 | 29-33 | 4 | 24,751 | Tony Armas | Brett Myers | Chad Cordero | Clay Condrey | | 284 | 291 | -7 |
| 2006-06-10 | vs PHI | 63 | L 2-6 | 29-34 | 4 | 32,089 | Livan Hernandez | Cory Lidle | Geoff Geary | Livan Hernandez | | 286 | 297 | -11 |
| 2006-06-11 | vs PHI | 64 | W 6-0 | 30-34 | 4 | 30,583 | Shawn Hill | Cole Hamels | Shawn Hill | Cole Hamels | | 292 | 297 | -5 |
| 2006-06-12 | vs COL | 65 | L 3-4 | 30-35 | 4 | 20,633 | Ramon Ortiz | Jeff Francis | Jeff Francis | Ramon Ortiz | Brian Fuentes | 295 | 301 | -6 |
| 2006-06-13 | vs COL | 66 | L 2-9 | 30-36 | 4 | 21,689 | Mike O'Connor | Josh Fogg | Josh Fogg | Mike O'Connor | | 297 | 310 | -13 |
| 2006-06-14 | vs COL | 67 | L 8-14 | 30-37 | 4 | 24,273 | Tony Armas | Byung-Hyun Kim | Tom Martin | Bill Bray | | 305 | 324 | -19 |
| 2006-06-15 | vs COL | 68 | L 1-8 | 30-38 | 4 | 22,793 | Livan Hernandez | Jason Jennings | Jason Jennings | Livan Hernandez | | 306 | 332 | -26 |
| 2006-06-16 | vs NYA | 69 | L 5-7 | 30-39 | 4 | 44,749 | Shawn Hill | Jaret Wright | Mariano Rivera | Chad Cordero | | 311 | 339 | -28 |
| 2006-06-17 | vs NYA | 70 | W 11-9 | 31-39 | 3 | 45,085 | Ramon Ortiz | Shawn Chacon | Jon Rauch | Mariano Rivera | Chad Cordero | 322 | 348 | -26 |
| 2006-06-18 | vs NYA | 71 | W 3-2 | 32-39 | 3 | 45,157 | Mike O'Connor | Chien-Ming Wang | Gary Majewski | Chien-Ming Wang | | 325 | 350 | -25 |
| 2006-06-19 | @ BOS | 72 | L 3-6 | 32-40 | 3 | 36,252 | Tony Armas | Kyle Snyder | Kyle Snyder | Tony Armas | Mike Timlin | 328 | 356 | -28 |
| 2006-06-20 | @ BOS | 73 | L 3-11 | 32-41 | 4 | 36,421 | Livan Hernandez | Tim Wakefield | Tim Wakefield | Livan Hernandez | | 331 | 367 | -36 |
| 2006-06-21 | @ BOS | 74 | L 3-9 | 32-42 | 4 | 36,464 | Shawn Hill | Jon Lester | Jon Lester | Shawn Hill | | 334 | 376 | -42 |
| 2006-06-23 | @ BAL | 75 | L 1-2 | 32-43 | 4 | 48,331 | John Patterson | Rodrigo Lopez | Rodrigo Lopez | John Patterson | Chris Ray | 335 | 378 | -43 |
| 2006-06-24 | @ BAL | 76 | L 2-3 | 32-44 | 4 | 36,290 | Mike O'Connor | Adam Loewen | Todd Williams | Chad Cordero | | 337 | 381 | -44 |
| 2006-06-25 | @ BAL | 77 | W 9-5 | 33-44 | 4 | 27,680 | Livan Hernandez | Daniel Cabrera | Livan Hernandez | Daniel Cabrera | | 346 | 386 | -40 |
| 2006-06-27 | @ TOR | 78 | L 0-6 | 33-45 | 5 | 20,288 | Ramon Ortiz | A.J. Burnett | A.J. Burnett | Ramon Ortiz | | 346 | 392 | -46 |
| 2006-06-28 | @ TOR | 79 | L 1-6 | 33-46 | 5 | 17,067 | Shawn Hill | Ted Lilly | Ted Lilly | Shawn Hill | | 347 | 398 | -51 |
| 2006-06-29 | @ TOR | 80 | L 4-8 | 33-47 | 5 | 17,175 | John Patterson | Roy Halladay | Roy Halladay | John Patterson | | 351 | 406 | -55 |
| 2006-06-30 | vs TBA | 81 | L 1-11 | 33-48 | 5 | 21,854 | Mike O'Connor | Tim Corcoran | Tim Corcoran | Mike O'Connor | | 352 | 417 | -65 |
| 2006-07-01 | vs TBA | 82 | W 4-3 | 34-48 | 5 | 21,515 | Livan Hernandez | James Shields | Chad Cordero | Brian Meadows | | 356 | 420 | -64 |
| 2006-07-02 | vs TBA | 83 | W 6-2 | 35-48 | 5 | 23,823 | Ramon Ortiz | Jae Weong Seo | Ramon Ortiz | Jae Weong Seo | | 362 | 422 | -60 |
| 2006-07-03 | vs FLO | 84 | W 9-1 | 36-48 | 5 | 24,943 | Pedro Astacio | Ricky Nolasco | Pedro Astacio | Ricky Nolasco | | 371 | 423 | -52 |
| 2006-07-04 | vs FLO | 85 | W 6-4 | 37-48 | 4 | 23,118 | John Patterson | Scott Olsen | Chad Cordero | Joe Borowski | | 377 | 427 | -50 |
| 2006-07-05 | vs FLO | 86 | L 9-18 | 37-49 | 5 | 18,441 | Mike O'Connor | Yusmeiro Petit | Yusmeiro Petit | Mike O'Connor | Renyel Pinto | 386 | 445 | -59 |
| 2006-07-06 | vs FLO | 87 | W 8-7 | 38-49 | 5 | 29,053 | Livan Hernandez | Anibal Sanchez | Chad Cordero | Jason Vargas | | 394 | 452 | -58 |
| 2006-07-07 | vs SDN | 88 | L 2-3 | 38-50 | 5 | 25,161 | Ramon Ortiz | Woody Williams | Woody Williams | Ramon Ortiz | Trevor Hoffman | 396 | 455 | -59 |
| 2006-07-08 | vs SDN | 89 | L 2-5 | 38-51 | 5 | 27,060 | Pedro Astacio | Chris Young | Chris Young | Pedro Astacio | Trevor Hoffman | 398 | 460 | -62 |
| 2006-07-09 | vs SDN | 90 | L 9-10 | 38-52 | 5 | 22,000 | John Patterson | Clay Hensley | Scott Cassidy | Chad Cordero | Scott Linebrink | 407 | 470 | -63 |
| 2006-07-14 | @ PIT | 91 | L 4-7 | 38-53 | 5 | 26,720 | Ramon Ortiz | Zach Duke | Zach Duke | Ramon Ortiz | Mike Gonzalez | 411 | 477 | -66 |
| 2006-07-15 | @ PIT | 92 | L 6-7 | 38-54 | 5 | 32,626 | Pedro Astacio | Ian Snell | Mike Gonzalez | Roy Corcoran | | 417 | 484 | -67 |
| 2006-07-16 | @ PIT | 93 | W 8-4 | 39-54 | 5 | 18,908 | Livan Hernandez | Paul Maholm | Mike Stanton | Roberto Hernandez | | 425 | 488 | -63 |
| 2006-07-17 | @ FLO | 94 | L 2-4 | 39-55 | 5 | 7,562 | Tony Armas | Ricky Nolasco | Ricky Nolasco | Tony Armas | Joe Borowski | 427 | 492 | -65 |
| 2006-07-18 | @ FLO | 95 | W 7-6 | 40-55 | 5 | 11,247 | Mike O'Connor | Dontrelle Willis | Mike Stanton | Logan Kensing | Chad Cordero | 434 | 498 | -64 |
| 2006-07-19 | @ FLO | 96 | L 0-1 | 40-56 | 5 | 25,546 | Ramon Ortiz | Anibal Sanchez | Anibal Sanchez | Ramon Ortiz | Joe Borowski | 434 | 499 | -65 |
| 2006-07-21 | vs CHN | 97 | W 7-6 | 41-56 | 5 | 35,442 | Pedro Astacio | Mark Prior | Jon Rauch | Bob Howry | Chad Cordero | 441 | 505 | -64 |
| 2006-07-22 | vs CHN | 98 | W 7-3 | 42-56 | 5 | 38,021 | Livan Hernandez | Sean Marshall | Livan Hernandez | Scott Williamson | | 448 | 508 | -60 |
| 2006-07-23 | vs CHN | 99 | W 7-1 | 43-56 | 5 | 30,851 | Tony Armas | Carlos Marmol | Tony Armas | Carlos Marmol | | 455 | 509 | -54 |
| 2006-07-25 | vs SFN | 100 | W 8-6 | 44-56 | 5 | 33,358 | Ramon Ortiz | Matt Morris | Ramon Ortiz | Matt Morris | Chad Cordero | 463 | 515 | -52 |
| 2006-07-26 | vs SFN | 101 | W 4-3 | 45-56 | 5 | 30,248 | Pedro Astacio | Noah Lowry | Saul Rivera | Armando Benitez | | 467 | 518 | -51 |
| 2006-07-27 | vs SFN | 102 | W 6-5 | 46-56 | 5 | 29,717 | Livan Hernandez | Matt Cain | Livan Hernandez | Matt Cain | Chad Cordero | 473 | 523 | -50 |
| 2006-07-28 | @ LAN | 103 | L 1-13 | 46-57 | 5 | 55,825 | Tony Armas | Chad Billingsley | Chad Billingsley | Tony Armas | | 474 | 536 | -62 |
| 2006-07-29 | @ LAN | 104 | L 5-7 | 46-58 | 5 | 41,540 | Mike O'Connor | Derek Lowe | Derek Lowe | Mike O'Connor | Jonathan Broxton | 479 | 543 | -64 |
| 2006-07-30 | @ LAN | 105 | L 3-4 | 46-59 | 5 | 43,346 | Ramon Ortiz | Mark Hendrickson | Jonathan Broxton | Jon Rauch | Takashi Saito | 482 | 547 | -65 |
| 2006-07-31 | @ SFN | 106 | W 10-7 | 47-59 | 5 | 37,106 | Pedro Astacio | Noah Lowry | Pedro Astacio | Noah Lowry | Chad Cordero | 492 | 554 | -62 |
| 2006-08-01 | @ SFN | 107 | W 4-1 | 48-59 | 5 | 37,258 | Livan Hernandez | Matt Cain | Livan Hernandez | Matt Cain | Chad Cordero | 496 | 555 | -59 |
| 2006-08-02 | @ SFN | 108 | L 6-8 | 48-60 | 5 | 38,283 | Tony Armas | Jason Schmidt | Jason Schmidt | Tony Armas | Mike Stanton | 502 | 563 | -61 |
| 2006-08-04 | @ SDN | 109 | W 6-2 | 49-60 | 5 | 36,538 | Ramon Ortiz | Chris Young | Ramon Ortiz | Chris Young | | 508 | 565 | -57 |
| 2006-08-05 | @ SDN | 110 | L 3-6 | 49-61 | 5 | 40,339 | Pedro Astacio | Mike Thompson | Alan Embree | Pedro Astacio | Trevor Hoffman | 511 | 571 | -60 |
| 2006-08-06 | @ SDN | 111 | L 2-3 | 49-62 | 5 | 35,648 | Livan Hernandez | Jake Peavy | Doug Brocail | Micah Bowie | | 513 | 574 | -61 |
| 2006-08-08 | vs FLO | 112 | L 2-4 | 49-63 | 5 | 24,922 | Tony Armas | Ricky Nolasco | Ricky Nolasco | Tony Armas | Joe Borowski | 515 | 578 | -63 |
| 2006-08-09 | vs FLO | 113 | W 5-2 | 50-63 | 5 | 21,390 | Ramon Ortiz | Dontrelle Willis | Ramon Ortiz | Dontrelle Willis | Chad Cordero | 520 | 580 | -60 |
| 2006-08-10 | vs FLO | 114 | L 6-9 | 50-64 | 5 | 21,304 | Pedro Astacio | Anibal Sanchez | Brian Moehler | Ryan Wagner | Joe Borowski | 526 | 589 | -63 |
| 2006-08-11 | vs NYN | 115 | W 2-1 | 51-64 | 5 | 29,414 | Billy Traber | Tom Glavine | Billy Traber | Tom Glavine | Chad Cordero | 528 | 590 | -62 |
| 2006-08-12 | vs NYN | 116 | L 4-6 | 51-65 | 5 | 42,507 | Jason Bergmann | John Maine | Pedro Feliciano | Chris Schroder | Billy Wagner | 532 | 596 | -64 |
| 2006-08-13 | vs NYN | 117 | L 1-3 | 51-66 | 5 | 37,732 | Tony Armas | Steve Trachsel | Chad Bradford | Jon Rauch | Billy Wagner | 533 | 599 | -66 |
| 2006-08-14 | vs ATL | 118 | L 4-10 | 51-67 | 5 | 21,550 | Ramon Ortiz | Chuck James | Chuck James | Ramon Ortiz | | 537 | 609 | -72 |
| 2006-08-15 | vs ATL | 119 | W 5-0 | 52-67 | 5 | 24,036 | Pedro Astacio | Lance Cormier | Pedro Astacio | Lance Cormier | | 542 | 609 | -67 |
| 2006-08-16 | vs ATL | 120 | W 9-6 | 53-67 | 5 | 28,094 | Billy Traber | John Smoltz | Billy Traber | John Smoltz | Chad Cordero | 551 | 615 | -64 |
| 2006-08-17 | vs ATL | 121 | L 0-5 | 53-68 | 5 | 29,007 | Jason Bergmann | Oscar Villarreal | Oscar Villarreal | Jason Bergmann | | 551 | 620 | -69 |
| 2006-08-18 | @ PHI | 122 | W 6-4 | 54-68 | 5 | 30,123 | Tony Armas | Brett Myers | Tony Armas | Brett Myers | Chad Cordero | 557 | 624 | -67 |
| 2006-08-19 | @ PHI | 123 | L 2-11 | 54-69 | 5 | 34,881 | Ramon Ortiz | Cole Hamels | Cole Hamels | Ramon Ortiz | | 559 | 635 | -76 |
| 2006-08-20 | @ PHI | 124 | L 10-12 | 54-70 | 5 | 36,023 | Pedro Astacio | Randy Wolf | Randy Wolf | Pedro Astacio | Arthur Rhodes | 569 | 647 | -78 |
| 2006-08-21 | @ FLO | 125 | L 1-3 | 54-71 | 5 | 9,316 | Billy Traber | Anibal Sanchez | Anibal Sanchez | Billy Traber | Joe Borowski | 570 | 650 | -80 |
| 2006-08-22 | @ FLO | 126 | L 5-7 | 54-72 | 5 | 10,260 | Jason Bergmann | Josh Johnson | Taylor Tankersley | Ryan Wagner | Joe Borowski | 575 | 657 | -82 |
| 2006-08-23 | @ FLO | 127 | L 7-9 | 54-73 | 5 | 11,318 | Tony Armas | Scott Olsen | Scott Olsen | Tony Armas | | 582 | 666 | -84 |
| 2006-08-25 | @ ATL | 128 | W 7-6 | 55-73 | 5 | 33,621 | Ramon Ortiz | Chuck James | Ryan Wagner | Chad Paronto | Saul Rivera | 589 | 672 | -83 |
| 2006-08-26 | @ ATL | 129 | L 1-10 | 55-74 | 5 | 38,610 | Pedro Astacio | John Smoltz | John Smoltz | Pedro Astacio | | 590 | 682 | -92 |
| 2006-08-27 | @ ATL | 130 | L 6-13 | 55-75 | 5 | 30,587 | Billy Traber | Oscar Villarreal | Macay McBride | Billy Traber | | 596 | 695 | -99 |
| 2006-08-29 | vs PHI | 131 | L 6-10 | 55-76 | 5 | 25,735 | Tony Armas | Brett Myers | Brett Myers | Tony Armas | Arthur Rhodes | 602 | 705 | -103 |
| 2006-08-30 | vs PHI | 132 | L 1-5 | 55-77 | 5 | 24,438 | Ramon Ortiz | Cole Hamels | Cole Hamels | Ramon Ortiz | | 603 | 710 | -107 |
| 2006-08-31 | vs PHI | 133 | W 6-5 | 56-77 | 5 | 22,221 | Pedro Astacio | Randy Wolf | Ryan Wagner | Aaron Fultz | | 609 | 715 | -106 |
| 2006-09-02 | vs ARI | 134 | W 7-6 | 58-77 | 5 | 22,012 | Billy Traber | Miguel Batista | Chad Cordero | Brandon Lyon | | 616 | 721 | -105 |
| 2006-09-02 | vs ARI | 135 | W 4-3 | 58-77 | 5 | 22,922 | Jason Bergmann | Livan Hernandez | Saul Rivera | Livan Hernandez | Chad Cordero | 620 | 724 | -104 |
| 2006-09-03 | vs ARI | 136 | W 5-3 | 59-77 | 5 | 30,771 | Tony Armas | Brandon Webb | Ryan Wagner | Brandon Webb | Jon Rauch | 625 | 727 | -102 |
| 2006-09-04 | vs SLN | 137 | W 4-1 | 60-77 | 5 | 31,092 | Ramon Ortiz | Jason Marquis | Ramon Ortiz | Jason Marquis | | 629 | 728 | -99 |
| 2006-09-05 | vs SLN | 138 | L 0-2 | 60-78 | 5 | 25,937 | Pedro Astacio | Jeff Suppan | Jeff Suppan | Pedro Astacio | Jason Isringhausen | 629 | 730 | -101 |
| 2006-09-06 | vs SLN | 139 | W 7-6 | 61-78 | 5 | 21,322 | Mike O'Connor | Chris Carpenter | Chad Cordero | Jason Isringhausen | | 636 | 736 | -100 |
| 2006-09-07 | @ COL | 140 | L 5-10 | 61-79 | 5 | 18,617 | Jason Bergmann | Aaron Cook | Manuel Corpas | Ryan Wagner | | 641 | 746 | -105 |
| 2006-09-08 | @ COL | 141 | L 8-11 | 61-80 | 5 | 22,214 | Tony Armas | Byung-Hyun Kim | Nate Field | Jon Rauch | Brian Fuentes | 649 | 757 | -108 |
| 2006-09-09 | @ COL | 142 | L 5-9 | 61-81 | 5 | 22,735 | Ramon Ortiz | Josh Fogg | Mike Venafro | Ramon Ortiz | | 654 | 766 | -112 |
| 2006-09-10 | @ COL | 143 | L 9-13 | 61-82 | 5 | 18,647 | Pedro Astacio | Jeff Francis | Jose Mesa | Chris Schroder | Brian Fuentes | 663 | 779 | -116 |
| 2006-09-11 | @ ARI | 144 | W 7-6 | 62-82 | 5 | 29,610 | Billy Traber | Claudio Vargas | Jon Rauch | Luis Vizcaino | Chad Cordero | 670 | 785 | -115 |
| 2006-09-12 | @ ARI | 145 | W 5-4 | 63-82 | 5 | 31,182 | Jason Bergmann | Miguel Batista | Felix Rodriguez | Tony Pena | Chad Cordero | 675 | 789 | -114 |
| 2006-09-13 | @ ARI | 146 | L 2-4 | 63-83 | 5 | 19,031 | Tony Armas | Livan Hernandez | Livan Hernandez | Tony Armas | Jose Valverde | 677 | 793 | -116 |
| 2006-09-15 | vs MIL | 147 | L 2-5 | 63-84 | 5 | 21,168 | Ramon Ortiz | Tomo Ohka | Carlos Villanueva | Ramon Ortiz | Francisco Cordero | 679 | 798 | -119 |
| 2006-09-16 | vs MIL | 148 | W 8-5 | 64-84 | 5 | 24,252 | Pedro Astacio | David Bush | Pedro Astacio | David Bush | Chad Cordero | 687 | 803 | -116 |
| 2006-09-17 | vs MIL | 149 | W 6-1 | 65-84 | 5 | 26,128 | Mike O'Connor | Doug Davis | Saul Rivera | Doug Davis | | 693 | 804 | -111 |
| 2006-09-18 | vs ATL | 150 | L 1-6 | 65-85 | 5 | 25,211 | Tony Armas | Kyle Davies | Kyle Davies | Tony Armas | | 694 | 810 | -116 |
| 2006-09-19 | vs ATL | 151 | W 9-2 | 66-85 | 5 | 20,596 | Beltran Perez | Chuck James | Beltran Perez | Chuck James | | 703 | 812 | -109 |
| 2006-09-20 | vs ATL | 152 | L 3-7 | 66-86 | 5 | 19,027 | Ramon Ortiz | Lance Cormier | Lance Cormier | Ramon Ortiz | | 706 | 819 | -113 |
| 2006-09-22 | @ NYN | 153 | W 3-2 | 67-86 | 5 | 42,788 | Pedro Astacio | Orlando Hernandez | Pedro Astacio | Orlando Hernandez | Chad Cordero | 709 | 821 | -112 |
| 2006-09-23 | @ NYN | 154 | L 6-12 | 67-87 | 5 | 45,247 | Mike O'Connor | John Maine | John Maine | Mike O'Connor | | 715 | 833 | -118 |
| 2006-09-24 | @ NYN | 155 | W 5-1 | 68-87 | 5 | 44,543 | Tony Armas | Steve Trachsel | Tony Armas | Steve Trachsel | | 720 | 834 | -114 |
| 2006-09-25 | @ NYN | 156 | W 7-3 | 69-87 | 5 | 34,027 | Beltran Perez | Tom Glavine | Beltran Perez | Tom Glavine | | 727 | 837 | -110 |
| 2006-09-26 | vs PHI | 157 | W 4-3 | 70-87 | 5 | 18,960 | Ramon Ortiz | Brett Myers | Ramon Ortiz | Brett Myers | Chad Cordero | 731 | 840 | -109 |
| 2006-09-27 | vs PHI | 158 | L 7-8 | 70-88 | 5 | 21,809 | Pedro Astacio | Cole Hamels | Clay Condrey | Jason Bergmann | Fabio Castro | 738 | 848 | -110 |
| 2006-09-28 | vs PHI | 159 | W 3-1 | 71-88 | 5 | 18,324 | Mike O'Connor | Jon Lieber | Billy Traber | Jon Lieber | Jon Rauch | 741 | 849 | -108 |
| 2006-09-29 | vs NYN | 160 | L 3-4 | 71-89 | 5 | 27,805 | Tony Armas | John Maine | Pedro Feliciano | Jon Rauch | Billy Wagner | 744 | 853 | -109 |
| 2006-09-30 | vs NYN | 161 | L 0-13 | 71-90 | 5 | 30,449 | Beltran Perez | Tom Glavine | Tom Glavine | Beltran Perez | | 744 | 866 | -122 |
| 2006-10-01 | vs NYN | 162 | L 2-6 | 71-91 | 5 | 29,044 | Ramon Ortiz | Oliver Perez | Guillermo Mota | Ramon Ortiz | | 746 | 872 | -126 |