| 2006-04-03 | vs ARI | 1 | W 3-2 | 1-0 | 1 | 47,278 | Jason Jennings | Brandon Webb | Mike DeJean | Jason Grimsley | | 3 | 2 | 1 |
| 2006-04-05 | vs ARI | 2 | L 2-4 | 1-1 | 2 | 18,553 | Aaron Cook | Orlando Hernandez | Orlando Hernandez | Aaron Cook | Jose Valverde | 5 | 6 | -1 |
| 2006-04-06 | vs ARI | 3 | L 5-12 | 1-2 | 4 | 18,406 | Jeff Francis | Miguel Batista | Miguel Batista | Jeff Francis | | 10 | 18 | -8 |
| 2006-04-07 | @ SDN | 4 | W 10-4 | 2-2 | 2 | 33,918 | Josh Fogg | Chris Young | Josh Fogg | Clay Hensley | | 20 | 22 | -2 |
| 2006-04-08 | @ SDN | 5 | W 12-4 | 3-2 | 1 | 29,629 | Zach Day | Dewon Brazelton | Zach Day | Dewon Brazelton | | 32 | 26 | 6 |
| 2006-04-09 | @ SDN | 6 | W 10-4 | 4-2 | 1 | 28,901 | Jason Jennings | Jake Peavy | Jason Jennings | Jake Peavy | | 42 | 30 | 12 |
| 2006-04-11 | @ ARI | 7 | W 6-5 | 5-2 | 1 | 37,355 | Aaron Cook | Orlando Hernandez | Aaron Cook | Orlando Hernandez | Brian Fuentes | 48 | 35 | 13 |
| 2006-04-12 | @ ARI | 8 | L 4-5 | 5-3 | 2 | 18,664 | Jeff Francis | Miguel Batista | Greg Aquino | Ray King | Jose Valverde | 52 | 40 | 12 |
| 2006-04-13 | @ ARI | 9 | W 5-3 | 6-3 | 1 | 18,745 | Josh Fogg | Russ Ortiz | Josh Fogg | Russ Ortiz | Brian Fuentes | 57 | 43 | 14 |
| 2006-04-14 | vs PHI | 10 | L 8-10 | 6-4 | 2 | 25,390 | Zach Day | Ryan Madson | Ryan Madson | Zach Day | Tom Gordon | 65 | 53 | 12 |
| 2006-04-15 | vs PHI | 11 | W 10-6 | 7-4 | 1 | 23,206 | Jason Jennings | Jon Lieber | Ray King | Jon Lieber | | 75 | 59 | 16 |
| 2006-04-16 | vs PHI | 12 | L 0-1 | 7-5 | 2 | 25,144 | Aaron Cook | Brett Myers | Brett Myers | Aaron Cook | Tom Gordon | 75 | 60 | 15 |
| 2006-04-17 | vs SDN | 13 | L 2-5 | 7-6 | 2 | 18,591 | Jeff Francis | Chris Young | Chris Young | Jeff Francis | Trevor Hoffman | 77 | 65 | 12 |
| 2006-04-18 | vs SDN | 14 | W 3-2 | 8-6 | 2 | 18,595 | Josh Fogg | Clay Hensley | David Cortes | Jon Adkins | | 80 | 67 | 13 |
| 2006-04-19 | vs SDN | 15 | L 4-13 | 8-7 | 2 | 18,827 | Zach Day | Chan Ho Park | Chan Ho Park | Zach Day | | 84 | 80 | 4 |
| 2006-04-21 | vs SFN | 16 | W 9-8 | 9-7 | 1 | 30,339 | Jason Jennings | Jason Schmidt | David Cortes | Tim Worrell | | 93 | 88 | 5 |
| 2006-04-22 | vs SFN | 17 | L 4-6 | 9-8 | 2 | 36,035 | Aaron Cook | Brad Hennessey | Brad Hennessey | Aaron Cook | Armando Benitez | 97 | 94 | 3 |
| 2006-04-23 | vs SFN | 18 | W 3-2 | 10-8 | 1 | 30,310 | Jeff Francis | Matt Morris | David Cortes | Jeff Fassero | | 100 | 96 | 4 |
| 2006-04-24 | @ PHI | 19 | L 5-6 | 10-9 | 2 | 20,244 | Josh Fogg | Cory Lidle | Cory Lidle | Josh Fogg | Tom Gordon | 105 | 102 | 3 |
| 2006-04-25 | @ PHI | 20 | W 7-6 | 11-9 | 1 | 19,512 | Miguel Asencio | Gavin Floyd | Ramon Ramirez | Gavin Floyd | Brian Fuentes | 112 | 108 | 4 |
| 2006-04-26 | @ PHI | 21 | L 5-9 | 11-10 | 1 | 19,182 | Jason Jennings | Ryan Madson | Ryan Madson | Jason Jennings | | 117 | 117 | 0 |
| 2006-04-27 | @ PHI | 22 | W 6-3 | 12-10 | 1 | 21,506 | Aaron Cook | Jon Lieber | Aaron Cook | Ryan Franklin | Brian Fuentes | 123 | 120 | 3 |
| 2006-04-28 | @ FLO | 23 | W 3-2 | 13-10 | 1 | 10,419 | Jeff Francis | Brian Moehler | Brian Fuentes | Matt Herges | Scott Dohmann | 126 | 122 | 4 |
| 2006-04-29 | @ FLO | 24 | W 8-7 | 14-10 | 1 | 15,405 | Josh Fogg | Jason Vargas | Miguel Asencio | Randy Messenger | Brian Fuentes | 134 | 129 | 5 |
| 2006-04-30 | @ FLO | 25 | W 3-1 | 15-10 | 1 | 13,259 | Byung-Hyun Kim | Sergio Mitre | Byung-Hyun Kim | Sergio Mitre | Jose Mesa | 137 | 130 | 7 |
| 2006-05-01 | @ ATL | 26 | L 0-2 | 15-11 | 1 | 19,212 | Jason Jennings | Tim Hudson | Tim Hudson | Jason Jennings | | 137 | 132 | 5 |
| 2006-05-02 | @ ATL | 27 | L 4-5 | 15-12 | 1 | 22,813 | Aaron Cook | Jorge Sosa | Lance Cormier | Ray King | Chris Reitsma | 141 | 137 | 4 |
| 2006-05-03 | vs CIN | 28 | W 3-0 | 16-12 | 1 | 18,214 | Jeff Francis | Brandon Claussen | Jeff Francis | Brandon Claussen | Brian Fuentes | 144 | 137 | 7 |
| 2006-05-04 | vs CIN | 29 | L 1-7 | 16-13 | 2 | 18,204 | Josh Fogg | Aaron Harang | Aaron Harang | Josh Fogg | | 145 | 144 | 1 |
| 2006-05-05 | vs HOU | 30 | W 5-4 | 17-13 | 2 | 20,327 | Byung-Hyun Kim | Taylor Buchholz | Ramon Ramirez | Brad Lidge | | 150 | 148 | 2 |
| 2006-05-06 | vs HOU | 31 | W 5-0 | 18-13 | 2 | 26,358 | Jason Jennings | Wandy Rodriguez | Jason Jennings | Wandy Rodriguez | | 155 | 148 | 7 |
| 2006-05-07 | vs HOU | 32 | W 5-3 | 19-13 | 1 | 30,270 | Aaron Cook | Fernando Nieve | Aaron Cook | Fernando Nieve | Brian Fuentes | 160 | 151 | 9 |
| 2006-05-08 | @ SLN | 33 | W 6-2 | 20-13 | 1 | 39,007 | Jeff Francis | Jason Marquis | Jeff Francis | Jason Marquis | Brian Fuentes | 166 | 153 | 13 |
| 2006-05-09 | @ SLN | 34 | L 2-4 | 20-14 | 1 | 40,375 | Josh Fogg | Chris Carpenter | Adam Wainwright | Jose Mesa | Jason Isringhausen | 168 | 157 | 11 |
| 2006-05-10 | @ SLN | 35 | L 4-7 | 20-15 | 1 | 39,108 | Byung-Hyun Kim | Jeff Suppan | Jeff Suppan | Byung-Hyun Kim | Jason Isringhausen | 172 | 164 | 8 |
| 2006-05-12 | @ HOU | 36 | L 2-12 | 20-16 | 1 | 39,617 | Jason Jennings | Fernando Nieve | Mike Gallo | Jason Jennings | | 174 | 176 | -2 |
| 2006-05-13 | @ HOU | 37 | W 2-1 | 21-16 | 1 | 35,852 | Aaron Cook | Roy Oswalt | Aaron Cook | Roy Oswalt | Brian Fuentes | 176 | 177 | -1 |
| 2006-05-14 | @ HOU | 38 | L 0-3 | 21-17 | 2 | 37,614 | Jeff Francis | Andy Pettitte | Andy Pettitte | Jeff Francis | | 176 | 180 | -4 |
| 2006-05-15 | vs LAN | 39 | L 4-5 | 21-18 | 3 | 20,208 | Josh Fogg | Brett Tomko | Brett Tomko | Ramon Ramirez | Takashi Saito | 180 | 185 | -5 |
| 2006-05-16 | vs LAN | 40 | W 5-1 | 22-18 | 2 | 23,192 | Byung-Hyun Kim | Derek Lowe | Byung-Hyun Kim | Derek Lowe | | 185 | 186 | -1 |
| 2006-05-17 | vs LAN | 41 | L 2-3 | 22-19 | 3 | 30,296 | Jason Jennings | Brad Penny | Brad Penny | Jason Jennings | Danys Baez | 187 | 189 | -2 |
| 2006-05-19 | vs TOR | 42 | W 8-3 | 23-19 | 2 | 26,011 | Aaron Cook | Josh Towers | Aaron Cook | Josh Towers | | 195 | 192 | 3 |
| 2006-05-20 | vs TOR | 43 | W 5-1 | 24-19 | 2 | 26,212 | Jeff Francis | Ty Taubenheim | Jeff Francis | Ty Taubenheim | | 200 | 193 | 7 |
| 2006-05-21 | vs TOR | 44 | W 5-3 | 25-19 | 1 | 30,291 | Josh Fogg | Ted Lilly | Josh Fogg | Ted Lilly | Brian Fuentes | 205 | 196 | 9 |
| 2006-05-22 | @ LAN | 45 | L 1-6 | 25-20 | 2 | 33,652 | Byung-Hyun Kim | Jae Weong Seo | Jae Weong Seo | Byung-Hyun Kim | | 206 | 202 | 4 |
| 2006-05-23 | @ LAN | 46 | L 1-8 | 25-21 | 3 | 40,228 | Jason Jennings | Brad Penny | Brad Penny | Jason Jennings | | 207 | 210 | -3 |
| 2006-05-24 | @ LAN | 47 | L 1-7 | 25-22 | 3 | 39,299 | Aaron Cook | Aaron Sele | Aaron Sele | Aaron Cook | | 208 | 217 | -9 |
| 2006-05-26 | @ SFN | 48 | L 0-9 | 25-23 | 3 | 40,923 | Jeff Francis | Jason Schmidt | Jason Schmidt | Jeff Francis | | 208 | 226 | -18 |
| 2006-05-27 | @ SFN | 49 | L 1-4 | 25-24 | 4 | 40,350 | Josh Fogg | Matt Cain | Matt Cain | Josh Fogg | Armando Benitez | 209 | 230 | -21 |
| 2006-05-28 | @ SFN | 50 | W 6-3 | 26-24 | 3 | 42,935 | Byung-Hyun Kim | Jamey Wright | Byung-Hyun Kim | Jamey Wright | Brian Fuentes | 215 | 233 | -18 |
| 2006-05-29 | @ SDN | 51 | W 5-0 | 27-24 | 3 | 27,904 | Jason Jennings | Mike Thompson | Jason Jennings | Mike Thompson | | 220 | 233 | -13 |
| 2006-05-30 | @ SDN | 52 | L 0-2 | 27-25 | 3 | 23,698 | Aaron Cook | Chris Young | Chris Young | Aaron Cook | Trevor Hoffman | 220 | 235 | -15 |
| 2006-05-31 | @ SDN | 53 | L 2-3 | 27-26 | 4 | 24,607 | Jeff Francis | Clay Hensley | Clay Hensley | Jeff Francis | Trevor Hoffman | 222 | 238 | -16 |
| 2006-06-02 | vs FLO | 54 | L 2-4 | 27-27 | 5 | 26,112 | Josh Fogg | Dontrelle Willis | Dontrelle Willis | Josh Fogg | Logan Kensing | 224 | 242 | -18 |
| 2006-06-03 | vs FLO | 55 | L 0-13 | 27-28 | 5 | 23,831 | Byung-Hyun Kim | Ricky Nolasco | Ricky Nolasco | Byung-Hyun Kim | | 224 | 255 | -31 |
| 2006-06-04 | vs FLO | 56 | L 3-4 | 27-29 | 5 | 21,125 | Jason Jennings | Scott Olsen | Scott Olsen | Jason Jennings | Joe Borowski | 227 | 259 | -32 |
| 2006-06-05 | vs PIT | 57 | L 2-5 | 27-30 | 5 | 20,152 | Aaron Cook | Ian Snell | Ian Snell | Aaron Cook | Mike Gonzalez | 229 | 264 | -35 |
| 2006-06-06 | vs PIT | 58 | W 5-4 | 28-30 | 5 | 20,277 | Jeff Francis | Paul Maholm | Jeff Francis | Paul Maholm | Brian Fuentes | 234 | 268 | -34 |
| 2006-06-07 | vs PIT | 59 | W 16-9 | 29-30 | 5 | 21,509 | Josh Fogg | Oliver Perez | Scott Dohmann | Oliver Perez | | 250 | 277 | -27 |
| 2006-06-09 | vs LAN | 60 | L 0-3 | 29-31 | 5 | 30,455 | Byung-Hyun Kim | Brad Penny | Brad Penny | Byung-Hyun Kim | Takashi Saito | 250 | 280 | -30 |
| 2006-06-10 | vs LAN | 61 | W 12-9 | 30-31 | 5 | 35,557 | Jason Jennings | Brett Tomko | Jason Jennings | Brett Tomko | Brian Fuentes | 262 | 289 | -27 |
| 2006-06-11 | vs LAN | 62 | L 5-6 | 30-32 | 5 | 29,221 | Aaron Cook | Derek Lowe | Danys Baez | Brian Fuentes | Takashi Saito | 267 | 295 | -28 |
| 2006-06-12 | @ WAS | 63 | W 4-3 | 31-32 | 5 | 20,633 | Jeff Francis | Ramon Ortiz | Jeff Francis | Ramon Ortiz | Brian Fuentes | 271 | 298 | -27 |
| 2006-06-13 | @ WAS | 64 | W 9-2 | 32-32 | 4 | 21,689 | Josh Fogg | Mike O'Connor | Josh Fogg | Mike O'Connor | | 280 | 300 | -20 |
| 2006-06-14 | @ WAS | 65 | W 14-8 | 33-32 | 4 | 24,273 | Byung-Hyun Kim | Tony Armas | Tom Martin | Bill Bray | | 294 | 308 | -14 |
| 2006-06-15 | @ WAS | 66 | W 8-1 | 34-32 | 3 | 22,793 | Jason Jennings | Livan Hernandez | Jason Jennings | Livan Hernandez | | 302 | 309 | -7 |
| 2006-06-16 | @ SLN | 67 | L 1-8 | 34-33 | 4 | 45,736 | Aaron Cook | Jason Marquis | Jason Marquis | Aaron Cook | | 303 | 317 | -14 |
| 2006-06-17 | @ SLN | 68 | L 5-6 | 34-34 | 4 | 45,968 | Jeff Francis | Jeff Suppan | Jeff Suppan | Jeff Francis | Jason Isringhausen | 308 | 323 | -15 |
| 2006-06-18 | @ SLN | 69 | L 1-4 | 34-35 | 4 | 45,647 | Josh Fogg | Chris Carpenter | Chris Carpenter | Josh Fogg | Jason Isringhausen | 309 | 327 | -18 |
| 2006-06-19 | vs OAK | 70 | W 7-0 | 35-35 | 4 | 21,964 | Byung-Hyun Kim | Dan Haren | Byung-Hyun Kim | Dan Haren | | 316 | 327 | -11 |
| 2006-06-20 | vs OAK | 71 | W 6-0 | 36-35 | 4 | 21,753 | Jason Jennings | Esteban Loaiza | Jason Jennings | Esteban Loaiza | | 322 | 327 | -5 |
| 2006-06-21 | vs OAK | 72 | L 2-3 | 36-36 | 4 | 26,489 | Aaron Cook | Barry Zito | Kiko Calero | Ray King | | 324 | 330 | -6 |
| 2006-06-23 | vs TEX | 73 | L 6-8 | 36-37 | 3 | 28,360 | Jeff Francis | John Koronka | John Koronka | Jeff Francis | Akinori Otsuka | 330 | 338 | -8 |
| 2006-06-24 | vs TEX | 74 | W 11-6 | 37-37 | 3 | 31,439 | Josh Fogg | Rob Tejeda | Josh Fogg | Rob Tejeda | | 341 | 344 | -3 |
| 2006-06-25 | vs TEX | 75 | W 3-0 | 38-37 | 3 | 28,313 | Byung-Hyun Kim | Vicente Padilla | Byung-Hyun Kim | Vicente Padilla | Brian Fuentes | 344 | 344 | 0 |
| 2006-06-26 | @ ANA | 76 | L 4-5 | 38-38 | 3 | 43,781 | Jason Jennings | John Lackey | John Lackey | Jose Mesa | Francisco Rodriguez | 348 | 349 | -1 |
| 2006-06-27 | @ ANA | 77 | W 12-4 | 39-38 | 3 | 39,341 | Aaron Cook | Jeff Weaver | Aaron Cook | Jeff Weaver | | 360 | 353 | 7 |
| 2006-06-28 | @ ANA | 78 | W 6-2 | 40-38 | 2 | 38,153 | Jeff Francis | Ervin Santana | Ramon Ramirez | Scot Shields | | 366 | 355 | 11 |
| 2006-06-30 | @ SEA | 79 | W 2-0 | 41-38 | 2 | 31,612 | Josh Fogg | Jamie Moyer | Josh Fogg | Jamie Moyer | | 368 | 355 | 13 |
| 2006-07-01 | @ SEA | 80 | L 7-8 | 41-39 | 2 | 33,638 | Byung-Hyun Kim | Joel Pineiro | Julio Mateo | David Cortes | J.J. Putz | 375 | 363 | 12 |
| 2006-07-02 | @ SEA | 81 | W 4-3 | 42-39 | 2 | 31,709 | Jason Jennings | Jarrod Washburn | Brian Fuentes | Julio Mateo | Ray King | 379 | 366 | 13 |
| 2006-07-03 | vs SFN | 82 | L 6-9 | 42-40 | 3 | 48,364 | Aaron Cook | Noah Lowry | Jeremy Accardo | Ramon Ramirez | Armando Benitez | 385 | 375 | 10 |
| 2006-07-04 | vs SFN | 83 | W 6-1 | 43-40 | 1 | 48,078 | Jeff Francis | Jason Schmidt | Jeff Francis | Jason Schmidt | | 391 | 376 | 15 |
| 2006-07-05 | vs SFN | 84 | W 5-3 | 44-40 | 1 | 23,485 | Josh Fogg | Jamey Wright | Josh Fogg | Jamey Wright | Brian Fuentes | 396 | 379 | 17 |
| 2006-07-07 | vs ARI | 85 | L 3-4 | 44-41 | 3 | 26,313 | Byung-Hyun Kim | Miguel Batista | Brandon Medders | Byung-Hyun Kim | Jorge Julio | 399 | 383 | 16 |
| 2006-07-08 | vs ARI | 86 | L 7-8 | 44-42 | 3 | 22,874 | Jason Jennings | Brandon Webb | Luis Vizcaino | Brian Fuentes | Jorge Julio | 406 | 391 | 15 |
| 2006-07-09 | vs ARI | 87 | L 5-8 | 44-43 | 3 | 22,210 | Aaron Cook | Juan Cruz | Edgar Gonzalez | Scott Dohmann | Jorge Julio | 411 | 399 | 12 |
| 2006-07-13 | @ CIN | 88 | L 7-9 | 44-44 | 4 | 20,660 | Jeff Francis | Eric Milton | Eric Milton | Jeff Francis | Eddie Guardado | 418 | 408 | 10 |
| 2006-07-14 | @ CIN | 89 | L 1-3 | 44-45 | 5 | 22,497 | Jason Jennings | Aaron Harang | Aaron Harang | Jason Jennings | Eddie Guardado | 419 | 411 | 8 |
| 2006-07-15 | @ CIN | 90 | L 2-3 | 44-46 | 5 | 35,396 | Aaron Cook | Bronson Arroyo | Bill Bray | Brian Fuentes | | 421 | 414 | 7 |
| 2006-07-16 | @ CIN | 91 | L 4-6 | 44-47 | 5 | 27,043 | Josh Fogg | Elizardo Ramirez | Todd Coffey | Jose Mesa | Eddie Guardado | 425 | 420 | 5 |
| 2006-07-17 | @ PIT | 92 | L 1-3 | 44-48 | 5 | 18,835 | Byung-Hyun Kim | Kip Wells | John Grabow | Byung-Hyun Kim | Matt Capps | 426 | 423 | 3 |
| 2006-07-18 | @ PIT | 93 | W 13-4 | 45-48 | 5 | 20,086 | Jeff Francis | Tom Gorzelanny | Jeff Francis | Tom Gorzelanny | | 439 | 427 | 12 |
| 2006-07-19 | @ PIT | 94 | L 5-6 | 45-49 | 5 | 19,881 | Jason Jennings | Zach Duke | Zach Duke | Jason Jennings | Mike Gonzalez | 444 | 433 | 11 |
| 2006-07-21 | @ ARI | 95 | L 2-6 | 45-50 | 5 | 23,068 | Aaron Cook | Claudio Vargas | Claudio Vargas | Aaron Cook | | 446 | 439 | 7 |
| 2006-07-22 | @ ARI | 96 | L 3-4 | 45-51 | 5 | 28,745 | Josh Fogg | Enrique Gonzalez | Brandon Medders | Jose Mesa | Jorge Julio | 449 | 443 | 6 |
| 2006-07-23 | @ ARI | 97 | W 9-7 | 46-51 | 5 | 29,310 | Byung-Hyun Kim | Juan Cruz | Tom Martin | Jorge Julio | Brian Fuentes | 458 | 450 | 8 |
| 2006-07-24 | vs SLN | 98 | W 7-0 | 47-51 | 4 | 28,830 | Jeff Francis | Anthony Reyes | Jeff Francis | Anthony Reyes | | 465 | 450 | 15 |
| 2006-07-25 | vs SLN | 99 | L 0-1 | 47-52 | 4 | 31,673 | Jason Jennings | Chris Carpenter | Chris Carpenter | Jason Jennings | Jason Isringhausen | 465 | 451 | 14 |
| 2006-07-26 | vs SLN | 100 | L 1-6 | 47-53 | 4 | 32,872 | Aaron Cook | Jeff Suppan | Jeff Suppan | Aaron Cook | | 466 | 457 | 9 |
| 2006-07-27 | vs SDN | 101 | W 9-8 | 48-53 | 4 | 24,260 | Josh Fogg | Woody Williams | Brian Fuentes | Scott Williamson | | 475 | 465 | 10 |
| 2006-07-28 | vs SDN | 102 | W 3-1 | 49-53 | 4 | 28,790 | Byung-Hyun Kim | Clay Hensley | Byung-Hyun Kim | Clay Hensley | Brian Fuentes | 478 | 466 | 12 |
| 2006-07-29 | vs SDN | 103 | L 2-4 | 49-54 | 4 | 43,433 | Jeff Francis | Chris Young | Chris Young | Jeff Francis | Trevor Hoffman | 480 | 470 | 10 |
| 2006-07-30 | vs SDN | 104 | W 3-1 | 50-54 | 4 | 25,790 | Jason Jennings | Mike Thompson | Jason Jennings | Mike Thompson | Brian Fuentes | 483 | 471 | 12 |
| 2006-07-31 | vs MIL | 105 | W 4-2 | 51-54 | 3 | 23,189 | Aaron Cook | Chris Capuano | Aaron Cook | Chris Capuano | Brian Fuentes | 487 | 473 | 14 |
| 2006-08-01 | vs MIL | 106 | L 0-1 | 51-55 | 3 | 22,082 | Josh Fogg | David Bush | David Bush | Josh Fogg | Francisco Cordero | 487 | 474 | 13 |
| 2006-08-02 | vs MIL | 107 | W 8-2 | 52-55 | 3 | 24,034 | Byung-Hyun Kim | Tomo Ohka | Byung-Hyun Kim | Tomo Ohka | | 495 | 476 | 19 |
| 2006-08-04 | @ SFN | 108 | W 5-2 | 53-55 | 4 | 38,033 | Jeff Francis | Matt Morris | Jeff Francis | Matt Morris | Brian Fuentes | 500 | 478 | 22 |
| 2006-08-05 | @ SFN | 109 | W 2-1 | 54-55 | 4 | 39,014 | Jason Jennings | Noah Lowry | Jeremy Affeldt | Brad Hennessey | Brian Fuentes | 502 | 479 | 23 |
| 2006-08-06 | @ SFN | 110 | L 2-6 | 54-56 | 4 | 39,288 | Aaron Cook | Matt Cain | Matt Cain | Aaron Cook | | 504 | 485 | 19 |
| 2006-08-07 | @ LAN | 111 | L 2-7 | 54-57 | 4 | 44,593 | Josh Fogg | Brad Penny | Brad Penny | Josh Fogg | | 506 | 492 | 14 |
| 2006-08-08 | @ LAN | 112 | L 2-4 | 54-58 | 4 | 50,210 | Byung-Hyun Kim | Greg Maddux | Brett Tomko | Byung-Hyun Kim | Takashi Saito | 508 | 496 | 12 |
| 2006-08-09 | @ LAN | 113 | W 3-1 | 55-58 | 4 | 46,643 | Jeff Francis | Derek Lowe | Jeremy Affeldt | Derek Lowe | Brian Fuentes | 511 | 497 | 14 |
| 2006-08-10 | @ LAN | 114 | L 3-4 | 55-59 | 4 | 48,699 | Jason Jennings | Chad Billingsley | Takashi Saito | Jose Mesa | | 514 | 501 | 13 |
| 2006-08-11 | vs CHN | 115 | W 10-2 | 56-59 | 4 | 35,744 | Aaron Cook | Rich Hill | Aaron Cook | Rich Hill | | 524 | 503 | 21 |
| 2006-08-12 | vs CHN | 116 | W 8-4 | 57-59 | 4 | 43,485 | Josh Fogg | Angel Guzman | Josh Fogg | Angel Guzman | | 532 | 507 | 25 |
| 2006-08-13 | vs CHN | 117 | L 7-8 | 57-60 | 4 | 35,408 | Byung-Hyun Kim | Carlos Marmol | Roberto Novoa | Manuel Corpas | Ryan Dempster | 539 | 515 | 24 |
| 2006-08-14 | vs ARI | 118 | W 4-3 | 58-60 | 4 | 21,365 | Jeff Francis | Claudio Vargas | Jeremy Affeldt | Tony Pena | | 543 | 518 | 25 |
| 2006-08-15 | vs ARI | 119 | L 1-2 | 58-61 | 4 | 22,076 | Jason Jennings | Miguel Batista | Brandon Medders | Ramon Ramirez | | 544 | 520 | 24 |
| 2006-08-16 | vs ARI | 120 | L 5-9 | 58-62 | 4 | 23,415 | Aaron Cook | Livan Hernandez | Livan Hernandez | Aaron Cook | | 549 | 529 | 20 |
| 2006-08-17 | vs ARI | 121 | W 8-4 | 59-62 | 4 | 23,390 | Josh Fogg | Brandon Webb | Josh Fogg | Brandon Webb | | 557 | 533 | 24 |
| 2006-08-18 | @ NYN | 122 | L 3-6 | 59-63 | 4 | 35,325 | Byung-Hyun Kim | Steve Trachsel | Steve Trachsel | Byung-Hyun Kim | Billy Wagner | 560 | 539 | 21 |
| 2006-08-19 | @ NYN | 123 | L 4-7 | 59-64 | 4 | 55,085 | Jeff Francis | David Williams | Aaron Heilman | Jeff Francis | Billy Wagner | 564 | 546 | 18 |
| 2006-08-20 | @ NYN | 124 | L 0-2 | 59-65 | 4 | 40,654 | Jason Jennings | Orlando Hernandez | Orlando Hernandez | Jason Jennings | Billy Wagner | 564 | 548 | 16 |
| 2006-08-22 | @ MIL | 125 | L 1-4 | 59-66 | 5 | 25,158 | Aaron Cook | Chris Capuano | Chris Capuano | Aaron Cook | Francisco Cordero | 565 | 552 | 13 |
| 2006-08-23 | @ MIL | 126 | L 1-7 | 59-67 | 5 | 35,569 | Byung-Hyun Kim | Ben Sheets | Ben Sheets | Byung-Hyun Kim | | 566 | 559 | 7 |
| 2006-08-24 | @ MIL | 127 | L 6-12 | 59-68 | 5 | 35,484 | Josh Fogg | Tomo Ohka | Tomo Ohka | Josh Fogg | | 572 | 571 | 1 |
| 2006-08-25 | vs SDN | 128 | W 13-5 | 60-68 | 5 | 24,182 | Jeff Francis | Mike Thompson | Jeff Francis | Mike Thompson | | 585 | 576 | 9 |
| 2006-08-26 | vs SDN | 129 | L 2-5 | 60-69 | 5 | 29,748 | Jason Jennings | Clay Hensley | Clay Hensley | Jason Jennings | Trevor Hoffman | 587 | 581 | 6 |
| 2006-08-27 | vs SDN | 130 | W 6-3 | 61-69 | 5 | 26,308 | Aaron Cook | Jake Peavy | Aaron Cook | Jake Peavy | | 593 | 584 | 9 |
| 2006-08-29 | vs NYN | 131 | L 5-10 | 61-70 | 5 | 23,454 | Byung-Hyun Kim | Steve Trachsel | Steve Trachsel | Byung-Hyun Kim | | 598 | 594 | 4 |
| 2006-08-30 | vs NYN | 132 | L 3-11 | 61-71 | 5 | 22,945 | Josh Fogg | David Williams | David Williams | Josh Fogg | | 601 | 605 | -4 |
| 2006-08-31 | vs NYN | 133 | W 8-4 | 62-71 | 5 | 23,273 | Jeff Francis | Oliver Perez | Jeff Francis | Oliver Perez | | 609 | 609 | 0 |
| 2006-09-01 | @ LAN | 134 | L 3-6 | 62-72 | 5 | 49,601 | Jason Jennings | Derek Lowe | Derek Lowe | Jason Jennings | Takashi Saito | 612 | 615 | -3 |
| 2006-09-02 | @ LAN | 135 | L 5-14 | 62-73 | 5 | 48,984 | Aaron Cook | Brad Penny | Brad Penny | Aaron Cook | | 617 | 629 | -12 |
| 2006-09-03 | @ LAN | 136 | W 12-5 | 63-73 | 5 | 44,895 | Byung-Hyun Kim | Aaron Sele | Byung-Hyun Kim | Aaron Sele | | 629 | 634 | -5 |
| 2006-09-04 | @ SDN | 137 | L 5-7 | 63-74 | 5 | 35,722 | Josh Fogg | Woody Williams | Rudy Seanez | Brian Fuentes | | 634 | 641 | -7 |
| 2006-09-05 | @ SDN | 138 | L 4-5 | 63-75 | 5 | 26,456 | Jeff Francis | Chris Young | Cla Meredith | Jeff Francis | Trevor Hoffman | 638 | 646 | -8 |
| 2006-09-06 | @ SDN | 139 | L 0-2 | 63-76 | 5 | 27,968 | Jason Jennings | Clay Hensley | Cla Meredith | Nate Field | | 638 | 648 | -10 |
| 2006-09-07 | vs WAS | 140 | W 10-5 | 64-76 | 5 | 18,617 | Aaron Cook | Jason Bergmann | Manuel Corpas | Ryan Wagner | | 648 | 653 | -5 |
| 2006-09-08 | vs WAS | 141 | W 11-8 | 65-76 | 5 | 22,214 | Byung-Hyun Kim | Tony Armas | Nate Field | Jon Rauch | Brian Fuentes | 659 | 661 | -2 |
| 2006-09-09 | vs WAS | 142 | W 9-5 | 66-76 | 5 | 22,735 | Josh Fogg | Ramon Ortiz | Mike Venafro | Ramon Ortiz | | 668 | 666 | 2 |
| 2006-09-10 | vs WAS | 143 | W 13-9 | 67-76 | 5 | 18,647 | Jeff Francis | Pedro Astacio | Jose Mesa | Chris Schroder | Brian Fuentes | 681 | 675 | 6 |
| 2006-09-12 | @ SFN | 144 | L 6-10 | 67-77 | 5 | 33,416 | Denny Bautista | Jonathan Sanchez | Kevin Correia | Denny Bautista | | 687 | 685 | 2 |
| 2006-09-13 | @ SFN | 145 | W 9-8 | 68-77 | 5 | 34,847 | Jason Jennings | Noah Lowry | Jason Jennings | Noah Lowry | Brian Fuentes | 696 | 693 | 3 |
| 2006-09-14 | @ SFN | 146 | L 0-5 | 68-78 | 5 | 35,167 | Aaron Cook | Matt Cain | Matt Cain | Aaron Cook | | 696 | 698 | -2 |
| 2006-09-15 | @ ARI | 147 | L 1-5 | 68-79 | 5 | 22,017 | Byung-Hyun Kim | Brandon Webb | Brandon Webb | Byung-Hyun Kim | | 697 | 703 | -6 |
| 2006-09-16 | @ ARI | 148 | L 6-7 | 68-80 | 5 | 27,822 | Josh Fogg | Claudio Vargas | Jorge Julio | Jeremy Affeldt | | 703 | 710 | -7 |
| 2006-09-17 | @ ARI | 149 | W 6-1 | 69-80 | 5 | 28,056 | Jeff Francis | Miguel Batista | Jeff Francis | Miguel Batista | | 709 | 711 | -2 |
| 2006-09-18 | vs SFN | 150 | W 20-8 | 70-80 | 5 | 18,346 | Justin Hampson | Noah Lowry | Justin Hampson | Noah Lowry | | 729 | 719 | 10 |
| 2006-09-19 | vs SFN | 151 | W 12-4 | 71-80 | 5 | 20,373 | Jason Jennings | Matt Cain | Jason Jennings | Matt Cain | Jeremy Affeldt | 741 | 723 | 18 |
| 2006-09-20 | vs SFN | 152 | L 4-7 | 71-81 | 5 | 19,324 | Aaron Cook | Jason Schmidt | Brian Wilson | Manuel Corpas | Mike Stanton | 745 | 730 | 15 |
| 2006-09-21 | vs ATL | 153 | L 3-6 | 71-82 | 5 | 18,499 | Byung-Hyun Kim | John Smoltz | John Smoltz | Byung-Hyun Kim | Bob Wickman | 748 | 736 | 12 |
| 2006-09-22 | vs ATL | 154 | W 6-4 | 72-82 | 5 | 33,260 | Josh Fogg | Tim Hudson | Josh Fogg | Tim Hudson | Brian Fuentes | 754 | 740 | 14 |
| 2006-09-23 | vs ATL | 155 | W 10-9 | 73-82 | 5 | 24,300 | Jeff Francis | Kyle Davies | Jeff Francis | Kyle Davies | Brian Fuentes | 764 | 749 | 15 |
| 2006-09-24 | vs ATL | 156 | W 9-8 | 74-82 | 4 | 30,216 | Juan Morillo | Chuck James | Jeremy Affeldt | Tyler Yates | Brian Fuentes | 773 | 757 | 16 |
| 2006-09-26 | vs LAN | 157 | L 4-11 | 74-83 | 5 | 20,133 | Jason Jennings | Greg Maddux | Greg Maddux | Jason Jennings | | 777 | 768 | 9 |
| 2006-09-27 | vs LAN | 158 | L 4-6 | 74-84 | 5 | 18,858 | Aaron Cook | Derek Lowe | Derek Lowe | Aaron Cook | Takashi Saito | 781 | 774 | 7 |
| 2006-09-28 | vs LAN | 159 | L 11-19 | 74-85 | 5 | 21,154 | Byung-Hyun Kim | Brad Penny | Mark Hendrickson | Ray King | | 792 | 793 | -1 |
| 2006-09-29 | @ CHN | 160 | W 5-2 | 75-85 | 5 | 33,721 | Josh Fogg | Carlos Zambrano | Josh Fogg | Carlos Zambrano | Brian Fuentes | 797 | 795 | 2 |
| 2006-09-30 | @ CHN | 161 | W 11-9 | 76-85 | 5 | 39,483 | Jeff Francis | Juan Mateo | Ramon Ramirez | Jae Kuk Ryu | | 808 | 804 | 4 |
| 2006-10-01 | @ CHN | 162 | L 5-8 | 76-86 | 5 | 39,609 | Ubaldo Jimenez | Wade Miller | David Aardsma | Jeremy Affeldt | | 813 | 812 | 1 |