| 2006-04-03 | vs SLN | 1 | L 5-13 | 0-1 | 4 | 44,614 | Jon Lieber | Chris Carpenter | Chris Carpenter | Jon Lieber | | 5 | 13 | -8 |
| 2006-04-05 | vs SLN | 2 | L 3-4 | 0-2 | 5 | 20,557 | Brett Myers | Mark Mulder | Brad Thompson | Tom Gordon | Jason Isringhausen | 8 | 17 | -9 |
| 2006-04-06 | vs SLN | 3 | L 2-4 | 0-3 | 5 | 20,413 | Cory Lidle | Jason Marquis | Jason Marquis | Cory Lidle | Jason Isringhausen | 10 | 21 | -11 |
| 2006-04-07 | vs LAN | 4 | L 3-5 | 0-4 | 5 | 25,518 | Gavin Floyd | Brett Tomko | Brett Tomko | Gavin Floyd | Danys Baez | 13 | 26 | -13 |
| 2006-04-09 | vs LAN | 5 | W 6-3 | 1-5 | 5 | 0 | Ryan Madson | Derek Lowe | Tom Gordon | Tim Hamulack | | 19 | 29 | -10 |
| 2006-04-09 | vs LAN | 6 | L 2-6 | 1-5 | 5 | 38,056 | Jon Lieber | Brad Penny | Brad Penny | Jon Lieber | | 21 | 35 | -14 |
| 2006-04-10 | @ ATL | 7 | L 3-5 | 1-6 | 5 | 47,332 | Brett Myers | John Thomson | Oscar Villarreal | Ryan Franklin | Chris Reitsma | 24 | 40 | -16 |
| 2006-04-12 | @ ATL | 8 | W 7-5 | 2-6 | 3 | 37,107 | Cory Lidle | Jorge Sosa | Cory Lidle | Jorge Sosa | Tom Gordon | 31 | 45 | -14 |
| 2006-04-13 | @ ATL | 9 | W 7-6 | 3-6 | 3 | 22,911 | Gavin Floyd | Kyle Davies | Gavin Floyd | Kyle Davies | Tom Gordon | 38 | 51 | -13 |
| 2006-04-14 | @ COL | 10 | W 10-8 | 4-6 | 3 | 25,390 | Ryan Madson | Zach Day | Ryan Madson | Zach Day | Tom Gordon | 48 | 59 | -11 |
| 2006-04-15 | @ COL | 11 | L 6-10 | 4-7 | 3 | 23,206 | Jon Lieber | Jason Jennings | Ray King | Jon Lieber | | 54 | 69 | -15 |
| 2006-04-16 | @ COL | 12 | W 1-0 | 5-7 | 3 | 25,144 | Brett Myers | Aaron Cook | Brett Myers | Aaron Cook | Tom Gordon | 55 | 69 | -14 |
| 2006-04-18 | vs WAS | 13 | L 3-10 | 5-8 | 3 | 20,072 | Cory Lidle | Tony Armas | Tony Armas | Cory Lidle | | 58 | 79 | -21 |
| 2006-04-19 | vs WAS | 14 | W 7-6 | 6-8 | 3 | 27,913 | Gavin Floyd | Livan Hernandez | Ryan Franklin | Mike Stanton | | 65 | 85 | -20 |
| 2006-04-20 | vs WAS | 15 | L 4-10 | 6-9 | 3 | 28,177 | Ryan Madson | Billy Traber | Billy Traber | Ryan Madson | | 69 | 95 | -26 |
| 2006-04-21 | vs FLO | 16 | L 3-4 | 6-10 | 4 | 20,227 | Jon Lieber | Scott Olsen | Scott Olsen | Jon Lieber | Joe Borowski | 72 | 99 | -27 |
| 2006-04-23 | vs FLO | 17 | W 4-2 | 7-10 | 3 | 40,383 | Brett Myers | Sergio Mitre | Brett Myers | Sergio Mitre | Tom Gordon | 76 | 101 | -25 |
| 2006-04-24 | vs COL | 18 | W 6-5 | 8-10 | 3 | 20,244 | Cory Lidle | Josh Fogg | Cory Lidle | Josh Fogg | Tom Gordon | 82 | 106 | -24 |
| 2006-04-25 | vs COL | 19 | L 6-7 | 8-11 | 3 | 19,512 | Gavin Floyd | Miguel Asencio | Ramon Ramirez | Gavin Floyd | Brian Fuentes | 88 | 113 | -25 |
| 2006-04-26 | vs COL | 20 | W 9-5 | 9-11 | 2 | 19,182 | Ryan Madson | Jason Jennings | Ryan Madson | Jason Jennings | | 97 | 118 | -21 |
| 2006-04-27 | vs COL | 21 | L 3-6 | 9-12 | 3 | 21,506 | Jon Lieber | Aaron Cook | Aaron Cook | Ryan Franklin | Brian Fuentes | 100 | 124 | -24 |
| 2006-04-28 | @ PIT | 22 | L 1-3 | 9-13 | 3 | 30,568 | Brett Myers | Ian Snell | Ian Snell | Brett Myers | Mike Gonzalez | 101 | 127 | -26 |
| 2006-04-29 | @ PIT | 23 | L 2-3 | 9-14 | 3 | 33,944 | Cory Lidle | Paul Maholm | Paul Maholm | Cory Lidle | Roberto Hernandez | 103 | 130 | -27 |
| 2006-04-30 | @ PIT | 24 | W 5-1 | 10-14 | 3 | 22,320 | Gavin Floyd | Oliver Perez | Gavin Floyd | Oliver Perez | | 108 | 131 | -23 |
| 2006-05-01 | @ FLO | 25 | W 8-5 | 11-14 | 3 | 6,017 | Ryan Madson | Dontrelle Willis | Rheal Cormier | Dontrelle Willis | Tom Gordon | 116 | 136 | -20 |
| 2006-05-02 | @ FLO | 26 | W 7-5 | 12-14 | 3 | 6,652 | Jon Lieber | Scott Olsen | Jon Lieber | Ricky Nolasco | Tom Gordon | 123 | 141 | -18 |
| 2006-05-03 | vs ATL | 27 | W 5-4 | 13-14 | 2 | 26,443 | Brett Myers | John Smoltz | Rheal Cormier | Mike Remlinger | Tom Gordon | 128 | 145 | -17 |
| 2006-05-04 | vs ATL | 28 | W 6-3 | 14-14 | 2 | 24,842 | Cory Lidle | John Thomson | Cory Lidle | John Thomson | Arthur Rhodes | 134 | 148 | -14 |
| 2006-05-05 | vs SFN | 29 | W 8-3 | 15-14 | 2 | 37,269 | Gavin Floyd | Matt Cain | Gavin Floyd | Matt Cain | | 142 | 151 | -9 |
| 2006-05-06 | vs SFN | 30 | W 4-1 | 16-14 | 2 | 44,042 | Ryan Madson | Jamey Wright | Ryan Madson | Jamey Wright | Tom Gordon | 146 | 152 | -6 |
| 2006-05-07 | vs SFN | 31 | W 9-5 | 17-14 | 2 | 39,315 | Jon Lieber | Matt Morris | Jon Lieber | Matt Morris | | 155 | 157 | -2 |
| 2006-05-09 | vs NYN | 32 | W 5-4 | 18-14 | 2 | 33,787 | Brett Myers | Pedro Martinez | Tom Gordon | Aaron Heilman | | 160 | 161 | -1 |
| 2006-05-10 | vs NYN | 33 | L 4-13 | 18-15 | 2 | 30,269 | Cory Lidle | Tom Glavine | Tom Glavine | Cory Lidle | | 164 | 174 | -10 |
| 2006-05-11 | vs NYN | 34 | W 2-0 | 19-15 | 2 | 28,224 | Gavin Floyd | Steve Trachsel | Gavin Floyd | Steve Trachsel | | 166 | 174 | -8 |
| 2006-05-12 | @ CIN | 35 | W 8-4 | 20-15 | 2 | 21,709 | Cole Hamels | Elizardo Ramirez | Ryan Madson | Elizardo Ramirez | Tom Gordon | 174 | 178 | -4 |
| 2006-05-13 | @ CIN | 36 | W 2-0 | 21-15 | 2 | 32,620 | Jon Lieber | David Williams | Jon Lieber | David Williams | Tom Gordon | 176 | 178 | -2 |
| 2006-05-14 | @ CIN | 37 | W 2-1 | 22-15 | 2 | 19,673 | Brett Myers | Brandon Claussen | Geoff Geary | Chris Hammond | Tom Gordon | 178 | 179 | -1 |
| 2006-05-16 | @ MIL | 38 | L 2-3 | 22-16 | 2 | 14,592 | Cory Lidle | Chris Capuano | Derrick Turnbow | Ryan Franklin | | 180 | 182 | -2 |
| 2006-05-17 | @ MIL | 39 | L 7-8 | 22-17 | 2 | 20,874 | Gavin Floyd | David Bush | Jose Capellan | Arthur Rhodes | | 187 | 190 | -3 |
| 2006-05-18 | @ MIL | 40 | L 4-5 | 22-18 | 2 | 27,419 | Cole Hamels | Dana Eveland | Justin Lehr | Ryan Madson | Derrick Turnbow | 191 | 195 | -4 |
| 2006-05-19 | vs BOS | 41 | L 3-5 | 22-19 | 2 | 44,296 | Jon Lieber | Matt Clement | Matt Clement | Jon Lieber | Jonathan Papelbon | 194 | 200 | -6 |
| 2006-05-20 | vs BOS | 42 | L 4-8 | 22-20 | 2 | 44,809 | Brett Myers | Josh Beckett | Josh Beckett | Brett Myers | | 198 | 208 | -10 |
| 2006-05-21 | vs BOS | 43 | W 10-5 | 23-20 | 2 | 44,738 | Cory Lidle | Lenny DiNardo | Cory Lidle | Lenny DiNardo | | 208 | 213 | -5 |
| 2006-05-23 | @ NYN | 44 | L 8-9 | 23-21 | 2 | 28,958 | Gavin Floyd | Steve Trachsel | Darren Oliver | Ryan Madson | | 216 | 222 | -6 |
| 2006-05-24 | @ NYN | 45 | L 4-5 | 23-22 | 2 | 32,094 | Jon Lieber | Alay Soler | Pedro Feliciano | Rheal Cormier | Billy Wagner | 220 | 227 | -7 |
| 2006-05-25 | @ NYN | 46 | W 5-3 | 24-22 | 2 | 51,365 | Brett Myers | Geremi Gonzalez | Brett Myers | Pedro Feliciano | Tom Gordon | 225 | 230 | -5 |
| 2006-05-26 | vs MIL | 47 | L 5-6 | 24-23 | 3 | 43,852 | Cory Lidle | Chris Capuano | Derrick Turnbow | Tom Gordon | Brian Shouse | 230 | 236 | -6 |
| 2006-05-27 | vs MIL | 48 | L 6-9 | 24-24 | 3 | 32,089 | Gavin Floyd | David Bush | Matt Wise | Ryan Franklin | Derrick Turnbow | 236 | 245 | -9 |
| 2006-05-28 | vs MIL | 49 | W 6-2 | 25-24 | 3 | 35,674 | Ryan Madson | Dana Eveland | Ryan Madson | Dana Eveland | | 242 | 247 | -5 |
| 2006-05-29 | vs WAS | 50 | W 11-2 | 26-24 | 3 | 33,682 | Jon Lieber | Mike O'Connor | Clay Condrey | Mike O'Connor | | 253 | 249 | 4 |
| 2006-05-30 | vs WAS | 51 | W 4-2 | 27-24 | 2 | 23,805 | Brett Myers | Tony Armas | Brett Myers | Tony Armas | Tom Gordon | 257 | 251 | 6 |
| 2006-05-31 | vs WAS | 52 | L 2-3 | 27-25 | 3 | 30,386 | Cory Lidle | Livan Hernandez | Livan Hernandez | Cory Lidle | Chad Cordero | 259 | 254 | 5 |
| 2006-06-01 | @ LAN | 53 | L 2-7 | 27-26 | 3 | 38,643 | Gavin Floyd | Derek Lowe | Derek Lowe | Gavin Floyd | | 261 | 261 | 0 |
| 2006-06-02 | @ LAN | 54 | W 8-6 | 28-26 | 3 | 55,142 | Ryan Madson | Jae Weong Seo | Geoff Geary | Danys Baez | Tom Gordon | 269 | 267 | 2 |
| 2006-06-03 | @ LAN | 55 | L 2-8 | 28-27 | 2 | 46,561 | Eude Brito | Brad Penny | Brad Penny | Eude Brito | | 271 | 275 | -4 |
| 2006-06-04 | @ LAN | 56 | W 6-4 | 29-27 | 2 | 48,270 | Brett Myers | Aaron Sele | Geoff Geary | Joe Beimel | Tom Gordon | 277 | 279 | -2 |
| 2006-06-05 | @ ARI | 57 | W 4-3 | 30-27 | 2 | 20,644 | Cory Lidle | Brandon Webb | Aaron Fultz | Brandon Lyon | Tom Gordon | 281 | 282 | -1 |
| 2006-06-06 | @ ARI | 58 | W 10-1 | 31-27 | 2 | 22,661 | Cole Hamels | Russ Ortiz | Cole Hamels | Russ Ortiz | | 291 | 283 | 8 |
| 2006-06-07 | @ ARI | 59 | W 7-3 | 32-27 | 2 | 21,031 | Ryan Madson | Dustin Nippert | Ryan Madson | Dustin Nippert | | 298 | 286 | 12 |
| 2006-06-08 | @ WAS | 60 | L 2-5 | 32-28 | 2 | 24,669 | Eude Brito | Mike O'Connor | Mike O'Connor | Eude Brito | Chad Cordero | 300 | 291 | 9 |
| 2006-06-09 | @ WAS | 61 | L 8-9 | 32-29 | 2 | 24,751 | Brett Myers | Tony Armas | Chad Cordero | Clay Condrey | | 308 | 300 | 8 |
| 2006-06-10 | @ WAS | 62 | W 6-2 | 33-29 | 2 | 32,089 | Cory Lidle | Livan Hernandez | Geoff Geary | Livan Hernandez | | 314 | 302 | 12 |
| 2006-06-11 | @ WAS | 63 | L 0-6 | 33-30 | 2 | 30,583 | Cole Hamels | Shawn Hill | Shawn Hill | Cole Hamels | | 314 | 308 | 6 |
| 2006-06-13 | vs NYN | 64 | L 7-9 | 33-31 | 2 | 37,964 | Ryan Madson | Tom Glavine | Chad Bradford | Ryan Madson | Billy Wagner | 321 | 317 | 4 |
| 2006-06-14 | vs NYN | 65 | L 3-9 | 33-32 | 2 | 38,811 | Brett Myers | Orlando Hernandez | Darren Oliver | Brett Myers | | 324 | 326 | -2 |
| 2006-06-15 | vs NYN | 66 | L 4-5 | 33-33 | 2 | 45,102 | Cory Lidle | Steve Trachsel | Steve Trachsel | Cory Lidle | Billy Wagner | 328 | 331 | -3 |
| 2006-06-16 | vs TBA | 67 | L 4-10 | 33-34 | 2 | 31,042 | Cole Hamels | James Shields | James Shields | Cole Hamels | | 332 | 341 | -9 |
| 2006-06-17 | vs TBA | 68 | L 2-7 | 33-35 | 2 | 35,939 | Scott Mathieson | Scott Kazmir | Scott Kazmir | Scott Mathieson | | 334 | 348 | -14 |
| 2006-06-18 | vs TBA | 69 | W 8-5 | 34-35 | 2 | 42,658 | Ryan Madson | Seth McClung | Ryan Madson | Seth McClung | Tom Gordon | 342 | 353 | -11 |
| 2006-06-19 | vs NYA | 70 | W 4-2 | 35-35 | 2 | 44,747 | Brett Myers | Randy Johnson | Brett Myers | Randy Johnson | Tom Gordon | 346 | 355 | -9 |
| 2006-06-20 | vs NYA | 71 | L 7-9 | 35-36 | 2 | 44,775 | Cory Lidle | Mike Mussina | T.J. Beam | Arthur Rhodes | Mariano Rivera | 353 | 364 | -11 |
| 2006-06-21 | vs NYA | 72 | L 0-5 | 35-37 | 2 | 45,111 | Cole Hamels | Jaret Wright | Jaret Wright | Cole Hamels | | 353 | 369 | -16 |
| 2006-06-23 | @ BOS | 73 | L 2-10 | 35-38 | 2 | 35,948 | Ryan Madson | Josh Beckett | Josh Beckett | Ryan Madson | | 355 | 379 | -24 |
| 2006-06-24 | @ BOS | 74 | L 3-5 | 35-39 | 2 | 35,564 | Brett Myers | Curt Schilling | Jonathan Papelbon | Tom Gordon | | 358 | 384 | -26 |
| 2006-06-26 | @ BOS | 75 | L 7-8 | 35-40 | 2 | 36,459 | Cory Lidle | Tim Wakefield | Craig Hansen | Clay Condrey | | 365 | 392 | -27 |
| 2006-06-28 | @ BAL | 76 | L 4-7 | 35-42 | 2 | 20,633 | Cole Hamels | Erik Bedard | Erik Bedard | Cole Hamels | Chris Ray | 369 | 399 | -30 |
| 2006-06-28 | @ BAL | 77 | L 5-12 | 35-42 | 2 | 26,228 | Scott Mathieson | Kris Benson | Kris Benson | Scott Mathieson | | 374 | 411 | -37 |
| 2006-06-29 | @ BAL | 78 | W 4-0 | 36-42 | 2 | 31,038 | Ryan Madson | Rodrigo Lopez | Ryan Madson | Rodrigo Lopez | Tom Gordon | 378 | 411 | -33 |
| 2006-06-30 | @ TOR | 79 | L 1-8 | 36-43 | 3 | 17,311 | Adam Bernero | Casey Janssen | Casey Janssen | Adam Bernero | | 379 | 419 | -40 |
| 2006-07-01 | @ TOR | 80 | L 2-5 | 36-44 | 3 | 24,248 | Cory Lidle | Ty Taubenheim | Scott Downs | Cory Lidle | B.J. Ryan | 381 | 424 | -43 |
| 2006-07-02 | @ TOR | 81 | W 11-6 | 37-44 | 2 | 26,177 | Aaron Fultz | A.J. Burnett | Geoff Geary | A.J. Burnett | | 392 | 430 | -38 |
| 2006-07-04 | vs SDN | 82 | W 6-5 | 38-44 | 2 | 29,192 | Cole Hamels | Clay Hensley | Tom Gordon | Cla Meredith | | 398 | 435 | -37 |
| 2006-07-05 | vs SDN | 83 | L 3-6 | 38-45 | 2 | 40,230 | Scott Mathieson | Jake Peavy | Scott Linebrink | Arthur Rhodes | Trevor Hoffman | 401 | 441 | -40 |
| 2006-07-06 | vs SDN | 84 | L 3-5 | 38-46 | 2 | 30,261 | Ryan Madson | Chan Ho Park | Chan Ho Park | Ryan Madson | Trevor Hoffman | 404 | 446 | -42 |
| 2006-07-07 | vs PIT | 85 | L 2-3 | 38-47 | 2 | 45,025 | Jon Lieber | Ian Snell | Ian Snell | Jon Lieber | Mike Gonzalez | 406 | 449 | -43 |
| 2006-07-08 | vs PIT | 86 | W 6-2 | 39-47 | 2 | 37,462 | Cory Lidle | Paul Maholm | Cory Lidle | Paul Maholm | | 412 | 451 | -39 |
| 2006-07-09 | vs PIT | 87 | W 8-3 | 40-47 | 2 | 32,527 | Cole Hamels | Zach Duke | Cole Hamels | Zach Duke | | 420 | 454 | -34 |
| 2006-07-14 | @ SFN | 88 | L 3-5 | 40-48 | 3 | 38,009 | Jon Lieber | Matt Morris | Matt Morris | Jon Lieber | Armando Benitez | 423 | 459 | -36 |
| 2006-07-15 | @ SFN | 89 | W 14-6 | 41-48 | 3 | 41,401 | Cory Lidle | Noah Lowry | Cory Lidle | Noah Lowry | | 437 | 465 | -28 |
| 2006-07-16 | @ SFN | 90 | W 6-2 | 42-48 | 3 | 38,241 | Brett Myers | Matt Cain | Brett Myers | Steve Kline | | 443 | 467 | -24 |
| 2006-07-17 | @ SDN | 91 | L 6-8 | 42-49 | 3 | 25,936 | Cole Hamels | Woody Williams | Alan Embree | Rheal Cormier | Trevor Hoffman | 449 | 475 | -26 |
| 2006-07-18 | @ SDN | 92 | L 6-10 | 42-50 | 3 | 33,327 | Ryan Madson | Clay Hensley | Clay Hensley | Ryan Madson | | 455 | 485 | -30 |
| 2006-07-19 | @ SDN | 93 | W 5-4 | 43-50 | 3 | 32,101 | Jon Lieber | Mike Thompson | Geoff Geary | Trevor Hoffman | Tom Gordon | 460 | 489 | -29 |
| 2006-07-21 | vs ATL | 94 | W 6-5 | 44-50 | 3 | 32,833 | Cory Lidle | John Smoltz | Cory Lidle | Ken Ray | Tom Gordon | 466 | 494 | -28 |
| 2006-07-23 | vs ATL | 95 | L 1-5 | 44-51 | 4 | 31,664 | Brett Myers | Horacio Ramirez | Macay McBride | Brett Myers | | 467 | 499 | -32 |
| 2006-07-24 | vs ATL | 96 | L 8-10 | 44-52 | 4 | 28,864 | Cole Hamels | Tim Hudson | Tim Hudson | Cole Hamels | Bob Wickman | 475 | 509 | -34 |
| 2006-07-25 | vs ARI | 97 | L 5-6 | 44-53 | 4 | 24,499 | Ryan Madson | Miguel Batista | Tony Pena | Ryan Franklin | | 480 | 515 | -35 |
| 2006-07-26 | vs ARI | 98 | W 6-4 | 45-53 | 4 | 45,459 | Jon Lieber | Brandon Webb | Jon Lieber | Brandon Webb | Tom Gordon | 486 | 519 | -33 |
| 2006-07-27 | vs ARI | 99 | W 5-2 | 46-53 | 4 | 31,752 | Cory Lidle | Claudio Vargas | Cory Lidle | Claudio Vargas | Tom Gordon | 491 | 521 | -30 |
| 2006-07-28 | vs FLO | 100 | L 1-4 | 46-54 | 4 | 25,105 | Brett Myers | Ricky Nolasco | Ricky Nolasco | Brett Myers | | 492 | 525 | -33 |
| 2006-07-29 | vs FLO | 101 | W 12-3 | 47-54 | 4 | 31,072 | Cole Hamels | Dontrelle Willis | Cole Hamels | Dontrelle Willis | | 504 | 528 | -24 |
| 2006-07-30 | vs FLO | 102 | W 11-5 | 49-54 | 2 | 31,375 | Randy Wolf | Anibal Sanchez | Aaron Fultz | Anibal Sanchez | | 515 | 533 | -18 |
| 2006-07-30 | vs FLO | 103 | W 9-2 | 49-54 | 2 | 23,604 | Ryan Madson | Brian Moehler | Ryan Madson | Brian Moehler | | 524 | 535 | -11 |
| 2006-07-31 | vs FLO | 104 | L 2-15 | 49-55 | 2 | 20,956 | Jon Lieber | Josh Johnson | Josh Johnson | Jon Lieber | | 526 | 550 | -24 |
| 2006-08-01 | @ SLN | 105 | W 5-3 | 50-55 | 2 | 42,773 | Scott Mathieson | Jeff Suppan | Scott Mathieson | Jeff Suppan | Tom Gordon | 531 | 553 | -22 |
| 2006-08-02 | @ SLN | 106 | W 16-8 | 51-55 | 2 | 42,598 | Brett Myers | Jeff Weaver | Brett Myers | Jeff Weaver | | 547 | 561 | -14 |
| 2006-08-03 | @ SLN | 107 | W 8-1 | 52-55 | 2 | 42,461 | Cole Hamels | Jason Marquis | Cole Hamels | Jason Marquis | | 555 | 562 | -7 |
| 2006-08-04 | @ NYN | 108 | W 5-3 | 53-55 | 2 | 43,209 | Randy Wolf | Orlando Hernandez | Ryan Madson | Darren Oliver | Tom Gordon | 560 | 565 | -5 |
| 2006-08-05 | @ NYN | 109 | L 3-4 | 53-56 | 2 | 44,829 | Jon Lieber | Tom Glavine | Tom Glavine | Jon Lieber | Billy Wagner | 563 | 569 | -6 |
| 2006-08-06 | @ NYN | 110 | L 1-8 | 53-57 | 2 | 39,144 | Scott Mathieson | John Maine | John Maine | Scott Mathieson | | 564 | 577 | -13 |
| 2006-08-07 | @ ATL | 111 | W 9-6 | 54-57 | 2 | 26,177 | Brett Myers | Horacio Ramirez | Brett Myers | Horacio Ramirez | | 573 | 583 | -10 |
| 2006-08-08 | @ ATL | 112 | L 1-3 | 54-58 | 2 | 30,714 | Cole Hamels | Tim Hudson | Tim Hudson | Cole Hamels | Bob Wickman | 574 | 586 | -12 |
| 2006-08-09 | @ ATL | 113 | W 9-3 | 55-58 | 2 | 27,222 | Randy Wolf | Chuck James | Rick White | Tyler Yates | | 583 | 589 | -6 |
| 2006-08-11 | vs CIN | 114 | W 6-5 | 56-58 | 2 | 41,461 | Jon Lieber | Kyle Lohse | Aaron Fultz | Elizardo Ramirez | | 589 | 594 | -5 |
| 2006-08-12 | vs CIN | 115 | L 7-9 | 56-59 | 2 | 39,553 | Scott Mathieson | Elizardo Ramirez | Chris Michalak | Tom Gordon | Eddie Guardado | 596 | 603 | -7 |
| 2006-08-13 | vs CIN | 116 | L 5-7 | 56-60 | 2 | 37,677 | Brett Myers | Eric Milton | Bill Bray | Ryan Madson | | 601 | 610 | -9 |
| 2006-08-14 | vs NYN | 117 | W 13-0 | 57-60 | 2 | 36,888 | Cole Hamels | Pedro Martinez | Cole Hamels | Pedro Martinez | | 614 | 610 | 4 |
| 2006-08-15 | vs NYN | 118 | W 11-4 | 58-60 | 2 | 40,283 | Randy Wolf | Orlando Hernandez | Randy Wolf | Orlando Hernandez | | 625 | 614 | 11 |
| 2006-08-16 | vs NYN | 119 | W 3-0 | 59-60 | 2 | 42,156 | Jon Lieber | Tom Glavine | Jon Lieber | Tom Glavine | | 628 | 614 | 14 |
| 2006-08-17 | vs NYN | 120 | L 2-7 | 59-61 | 2 | 45,775 | Scott Mathieson | John Maine | John Maine | Scott Mathieson | | 630 | 621 | 9 |
| 2006-08-18 | vs WAS | 121 | L 4-6 | 59-62 | 2 | 30,123 | Brett Myers | Tony Armas | Tony Armas | Brett Myers | Chad Cordero | 634 | 627 | 7 |
| 2006-08-19 | vs WAS | 122 | W 11-2 | 60-62 | 2 | 34,881 | Cole Hamels | Ramon Ortiz | Cole Hamels | Ramon Ortiz | | 645 | 629 | 16 |
| 2006-08-20 | vs WAS | 123 | W 12-10 | 61-62 | 2 | 36,023 | Randy Wolf | Pedro Astacio | Randy Wolf | Pedro Astacio | Arthur Rhodes | 657 | 639 | 18 |
| 2006-08-21 | @ CHN | 124 | W 6-5 | 62-62 | 2 | 38,950 | Jon Lieber | Rich Hill | Jon Lieber | Rich Hill | Arthur Rhodes | 663 | 644 | 19 |
| 2006-08-22 | @ CHN | 125 | W 6-3 | 63-62 | 2 | 38,770 | Jamie Moyer | Ryan O'Malley | Jamie Moyer | Ryan O'Malley | Ryan Madson | 669 | 647 | 22 |
| 2006-08-23 | @ CHN | 126 | W 2-1 | 64-62 | 2 | 39,470 | Brett Myers | Angel Guzman | Brett Myers | Bob Howry | Geoff Geary | 671 | 648 | 23 |
| 2006-08-24 | @ CHN | 127 | L 2-11 | 64-63 | 2 | 39,464 | Cole Hamels | Carlos Zambrano | Carlos Zambrano | Cole Hamels | | 673 | 659 | 14 |
| 2006-08-25 | @ NYN | 128 | W 4-3 | 65-63 | 2 | 41,707 | Randy Wolf | Brian Bannister | Randy Wolf | Brian Bannister | Ryan Madson | 677 | 662 | 15 |
| 2006-08-26 | @ NYN | 129 | L 5-11 | 65-64 | 2 | 47,019 | Jon Lieber | Oliver Perez | Pedro Feliciano | Rick White | | 682 | 673 | 9 |
| 2006-08-28 | @ NYN | 130 | L 3-8 | 65-65 | 2 | 45,868 | Jamie Moyer | John Maine | John Maine | Jamie Moyer | | 685 | 681 | 4 |
| 2006-08-29 | @ WAS | 131 | W 10-6 | 66-65 | 2 | 25,735 | Brett Myers | Tony Armas | Brett Myers | Tony Armas | Arthur Rhodes | 695 | 687 | 8 |
| 2006-08-30 | @ WAS | 132 | W 5-1 | 67-65 | 2 | 24,438 | Cole Hamels | Ramon Ortiz | Cole Hamels | Ramon Ortiz | | 700 | 688 | 12 |
| 2006-08-31 | @ WAS | 133 | L 5-6 | 67-66 | 2 | 22,221 | Randy Wolf | Pedro Astacio | Ryan Wagner | Aaron Fultz | | 705 | 694 | 11 |
| 2006-09-02 | vs ATL | 134 | L 3-4 | 68-67 | 2 | 31,717 | Jon Lieber | Oscar Villarreal | Tyler Yates | Arthur Rhodes | Bob Wickman | 708 | 698 | 10 |
| 2006-09-02 | vs ATL | 135 | W 16-4 | 68-67 | 2 | 28,600 | Scott Mathieson | Kyle Davies | Eude Brito | Kyle Davies | | 724 | 702 | 22 |
| 2006-09-03 | vs ATL | 136 | W 8-7 | 69-68 | 2 | 0 | Jamie Moyer | Tim Hudson | Geoff Geary | Bob Wickman | | 732 | 709 | 23 |
| 2006-09-03 | vs ATL | 137 | L 1-3 | 69-68 | 2 | 37,044 | Brett Myers | Lance Cormier | Chad Paronto | Geoff Geary | Bob Wickman | 733 | 712 | 21 |
| 2006-09-04 | vs HOU | 138 | W 3-2 | 70-68 | 2 | 44,674 | Cole Hamels | Roger Clemens | Rick White | Dave Borkowski | | 736 | 714 | 22 |
| 2006-09-06 | vs HOU | 139 | L 3-5 | 70-69 | 3 | 33,521 | Randy Wolf | Andy Pettitte | Dan Wheeler | Ryan Madson | Brad Lidge | 739 | 719 | 20 |
| 2006-09-07 | @ FLO | 140 | W 14-8 | 71-69 | 2 | 12,712 | Jon Lieber | Josh Johnson | Jon Lieber | Josh Johnson | | 753 | 727 | 26 |
| 2006-09-08 | @ FLO | 141 | W 3-2 | 72-69 | 2 | 21,432 | Jamie Moyer | Scott Olsen | Jamie Moyer | Scott Olsen | Tom Gordon | 756 | 729 | 27 |
| 2006-09-09 | @ FLO | 142 | L 3-4 | 72-70 | 2 | 27,444 | Brett Myers | Brian Moehler | Chris Resop | Arthur Rhodes | | 759 | 733 | 26 |
| 2006-09-10 | @ FLO | 143 | L 0-3 | 72-71 | 3 | 20,308 | Cole Hamels | Dontrelle Willis | Dontrelle Willis | Cole Hamels | | 759 | 736 | 23 |
| 2006-09-13 | @ ATL | 144 | W 6-5 | 74-71 | 2 | 0 | Randy Wolf | Kyle Davies | Rick White | Chad Paronto | Tom Gordon | 765 | 741 | 24 |
| 2006-09-13 | @ ATL | 145 | W 7-2 | 74-71 | 2 | 22,233 | Jon Lieber | Tim Hudson | Jon Lieber | Tim Hudson | | 772 | 743 | 29 |
| 2006-09-14 | @ ATL | 146 | L 1-4 | 74-72 | 2 | 19,352 | Jamie Moyer | Chuck James | Chuck James | Jamie Moyer | Bob Wickman | 773 | 747 | 26 |
| 2006-09-15 | @ HOU | 147 | W 4-3 | 75-72 | 2 | 41,432 | Brett Myers | Roger Clemens | Brett Myers | Roger Clemens | Tom Gordon | 777 | 750 | 27 |
| 2006-09-16 | @ HOU | 148 | W 7-2 | 76-72 | 2 | 41,002 | Cole Hamels | Jason Hirsh | Cole Hamels | Jason Hirsh | | 784 | 752 | 32 |
| 2006-09-17 | @ HOU | 149 | W 6-4 | 77-72 | 2 | 41,170 | Randy Wolf | Wandy Rodriguez | Randy Wolf | Wandy Rodriguez | Tom Gordon | 790 | 756 | 34 |
| 2006-09-18 | vs CHN | 150 | L 6-11 | 77-73 | 2 | 31,101 | Jon Lieber | Sean Marshall | Michael Wuertz | Jon Lieber | | 796 | 767 | 29 |
| 2006-09-19 | vs CHN | 151 | W 4-1 | 78-73 | 2 | 31,892 | Jamie Moyer | Wade Miller | Jamie Moyer | Wade Miller | Tom Gordon | 800 | 768 | 32 |
| 2006-09-20 | vs CHN | 152 | W 6-2 | 79-73 | 2 | 35,269 | Brett Myers | Les Walrond | Brett Myers | Les Walrond | | 806 | 770 | 36 |
| 2006-09-22 | vs FLO | 153 | W 5-2 | 80-73 | 2 | 44,737 | Cole Hamels | Ricky Nolasco | Cole Hamels | Ricky Nolasco | Tom Gordon | 811 | 772 | 39 |
| 2006-09-23 | vs FLO | 154 | W 8-6 | 81-73 | 2 | 37,055 | Jon Lieber | Brian Moehler | Jon Lieber | Brian Moehler | | 819 | 778 | 41 |
| 2006-09-24 | vs FLO | 155 | W 10-7 | 82-73 | 2 | 44,772 | Jamie Moyer | Scott Olsen | Jamie Moyer | Scott Olsen | | 829 | 785 | 44 |
| 2006-09-25 | vs HOU | 156 | L 4-5 | 82-74 | 2 | 44,688 | Randy Wolf | Chris Sampson | Dave Borkowski | Matt Smith | Dan Wheeler | 833 | 790 | 43 |
| 2006-09-26 | @ WAS | 157 | L 3-4 | 82-75 | 2 | 18,960 | Brett Myers | Ramon Ortiz | Ramon Ortiz | Brett Myers | Chad Cordero | 836 | 794 | 42 |
| 2006-09-27 | @ WAS | 158 | W 8-7 | 83-75 | 2 | 21,809 | Cole Hamels | Pedro Astacio | Clay Condrey | Jason Bergmann | Fabio Castro | 844 | 801 | 43 |
| 2006-09-28 | @ WAS | 159 | L 1-3 | 83-76 | 2 | 18,324 | Jon Lieber | Mike O'Connor | Billy Traber | Jon Lieber | Jon Rauch | 845 | 804 | 41 |
| 2006-09-29 | @ FLO | 160 | W 14-2 | 84-76 | 2 | 23,417 | Jamie Moyer | Brian Moehler | Jamie Moyer | Brian Moehler | | 859 | 806 | 53 |
| 2006-09-30 | @ FLO | 161 | W 4-3 | 85-76 | 2 | 20,992 | Randy Wolf | Scott Olsen | Ryan Madson | Scott Olsen | Tom Gordon | 863 | 809 | 54 |
| 2006-10-01 | @ FLO | 162 | L 2-3 | 85-77 | 2 | 36,768 | Brett Myers | Dontrelle Willis | Matt Herges | Fabio Castro | | 865 | 812 | 53 |