Passing
| Player | COM | ATT | YDS | PCT | YDS/A | LNG | TD | TD% | INT | INT% | SACK | SYDS | RAT |
| Alex Smith | 273 | 445 | 3144 | 61.3 | 7.1 | 56 | 17 | 3.5 | 5 | 1.1 | 44 | 263 | 90.7 |
| Josh Johnson | 19 | 36 | 246 | 52.8 | 6.8 | 42 | 1 | 2.8 | 2 | 5.6 | 3 | 24 | 60.6 |
| Colin Kaepernick | 3 | 5 | 35 | 60.0 | 7.0 | 19 | 0 | 0.0 | 0 | 0.0 | 0 | 0 | 81.3 |
| David Akers | 1 | 1 | 14 | 99.9 | 14.0 | 14 | 1 | 99.9 | 0 | 0.0 | 0 | 0 | 99.9 |
| Mario Manningham | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Vernon Davis | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Joe Hastings | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Kyle Williams | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Justin Peelle | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Delanie Walker | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Braylon Edwards | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Rock Cartwright | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Brett Swain | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Ted Ginn Jr. | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Frank Gore | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Kendall Hunter | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Isaac Sopoaga | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Michael Crabtree | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Joe Staley | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Brandon Jacobs | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Bruce Miller | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Andy Lee | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
| Anthony Dixon | 0 | 0 | 0 | 0.0 | -- | 0 | 0 | 0.0 | 0 | -- | 0 | 0 | 0.0 |
Rushing
| Player | ATT | YDS | YDS/A | LNG | TD | FUM | LST |
| Frank Gore | 282 | 1211 | 4.3 | 55 | 8 | 2 | 2 |
| Brandon Jacobs | 152 | 571 | 3.8 | 28 | 7 | 3 | 0 |
| Kendall Hunter | 112 | 473 | 4.2 | 44 | 2 | 0 | 0 |
| Alex Smith | 52 | 179 | 3.4 | 14 | 2 | 2 | 0 |
| Anthony Dixon | 29 | 87 | 3.0 | 9 | 2 | 0 | 0 |
| Ted Ginn Jr. | 8 | 68 | 8.5 | 24 | 0 | 0 | 0 |
| Josh Johnson | 11 | 67 | 6.1 | 14 | 0 | 1 | 1 |
| Rock Cartwright | 4 | 45 | 11.3 | 35 | 0 | 0 | 0 |
| Kyle Williams | 2 | 32 | 16.0 | 25 | 0 | 0 | 0 |
| Bruce Miller | 4 | 8 | 2.0 | 3 | 0 | 1 | 0 |
| Michael Crabtree | 1 | 6 | 6.0 | 6 | 0 | 0 | 0 |
| Delanie Walker | 3 | 5 | 1.7 | 14 | 0 | 0 | 0 |
| Braylon Edwards | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Joe Staley | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Justin Peelle | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Mario Manningham | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Isaac Sopoaga | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Brett Swain | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Joe Hastings | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| David Akers | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Colin Kaepernick | 2 | -2 | -1.0 | -1 | 0 | 0 | 0 |
| Vernon Davis | 2 | -5 | -2.5 | -2 | 0 | 0 | 0 |
| Andy Lee | 1 | -18 | -18.0 | -18 | 0 | 0 | 0 |
Receiving
| Player | REC | YDS | YDS/R | LNG | TD | FUM | LST |
| Michael Crabtree | 72 | 874 | 12.1 | 52 | 4 | 0 | 0 |
| Vernon Davis | 67 | 792 | 11.8 | 44 | 6 | 3 | 1 |
| Mario Manningham | 39 | 523 | 13.4 | 47 | 4 | 0 | 0 |
| Kyle Williams | 20 | 241 | 12.1 | 56 | 3 | 0 | 0 |
| Ted Ginn Jr. | 19 | 220 | 11.6 | 26 | 0 | 0 | 0 |
| Delanie Walker | 19 | 198 | 10.4 | 29 | 3 | 0 | 0 |
| Kendall Hunter | 16 | 195 | 12.2 | 44 | 0 | 0 | 0 |
| Braylon Edwards | 15 | 181 | 12.1 | 24 | 0 | 0 | 0 |
| Brandon Jacobs | 15 | 128 | 8.5 | 40 | 1 | 0 | 0 |
| Frank Gore | 17 | 114 | 6.7 | 13 | 0 | 0 | 0 |
| Bruce Miller | 11 | 83 | 7.6 | 30 | 1 | 0 | 0 |
| Rock Cartwright | 4 | 24 | 6.0 | 9 | 0 | 0 | 0 |
| Justin Peelle | 1 | 19 | 19.0 | 19 | 0 | 0 | 0 |
| Isaac Sopoaga | 1 | 18 | 18.0 | 18 | 0 | 0 | 0 |
| Joe Staley | 1 | 17 | 17.0 | 17 | 0 | 0 | 0 |
| Brett Swain | 2 | 15 | 7.5 | 9 | 0 | 0 | 0 |
| Anthony Dixon | 1 | 6 | 6.0 | 6 | 0 | 0 | 0 |
| Joe Hastings | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 |
| Colin Kaepernick | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Josh Johnson | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 |
| Andy Lee | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| Alex Smith | 0 | 0 | -- | 0 | 0 | 0 | 0 |
| David Akers | 0 | 0 | -- | 0 | 0 | 0 | 0 |
Field Goals
| Player | 1-19 | 20-29 | 30-39 | 40-49 | 50+ | FG | FGA | FG% | LG | XP% | PTS |
| David Akers | 2/2 | 16/16 | 13/14 | 6/11 | 7/9 | 44 | 52 | 84.6 | 55 | 99.9 | 166 |
| Andy Lee | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0 | 0 | 0.0 | 0 | 0.0 | 0 |
Punting
| Player | PUNTS | YDS | AVG | LNG | TB | TB% | IN20 | IN20% | RET | RETYDS | NET |
| Andy Lee | 78 | 3970 | 50.9 | 0 | 9 | 11.5 | 28 | 35.9 | 39 | 315 | 44.0 |
Punt Returns
| Player | PRET | FC | PRYDS | PRAVG | PRLG | PRTD |
| Ted Ginn Jr. | 38 | 18 | 466 | 12.3 | 0 | 1 |
| Kyle Williams | 2 | 4 | 41 | 20.5 | 36 | 0 |
| Kendall Hunter | ||||||
| Rock Cartwright |
Kick Returns
| Player | KRET | KRYDS | KRAVG | KRLG | KRTD |
| Ted Ginn Jr. | 29 | 800 | 27.6 | 0 | 1 |
| Kendall Hunter | 6 | 156 | 26.0 | 0 | 0 |
| Kyle Williams | 4 | 104 | 26.0 | 0 | 0 |
| Rock Cartwright | 3 | 15 | 5.0 | 0 | 0 |
Individual Defense
| Player | TOT | TAK | AST | SACKS | FUMREC |
| Carlos Rogers | 86 | 40 | 3 | 0.0 | 0 |
| Dashon Goldson | 128 | 52 | 12 | 0.0 | 1 |
| Tarell Brown | 80 | 36 | 4 | 0.0 | 0 |
| Donte Whitner | 124 | 49 | 13 | 0.0 | 3 |
| Tramaine Brock | 8 | 4 | 0 | 0.0 | 0 |
| Patrick Willis | 194 | 74 | 23 | 2.0 | 2 |
| Chris Culliver | 66 | 32 | 1 | 0.0 | 0 |
| Tavares Gooden | 2 | 1 | 0 | 0.0 | 0 |
| Ray McDonald | 78 | 29 | 10 | 5.5 | 1 |
| Delanie Walker | 0 | 0 | 0 | 0.0 | 1 |
| Demarcus Dobbs | 4 | 2 | 0 | 0.0 | 0 |
| Will Tukuafu | 4 | 2 | 0 | 0.0 | 1 |
| C.J. Spillman | 6 | 3 | 0 | 0.0 | 0 |
| Bruce Davis | 0 | 0 | 0 | 0.0 | 0 |
| Ahmad Brooks | 100 | 35 | 15 | 7.0 | 0 |
| Aldon Smith | 72 | 30 | 6 | 14.0 | 1 |
| Justin Smith | 116 | 45 | 13 | 7.5 | 1 |
| Navorro Bowman | 272 | 107 | 29 | 2.0 | 3 |
| Larry Grant | 64 | 24 | 8 | 2.0 | 0 |
| Parys Haralson | 62 | 25 | 6 | 2.0 | 0 |
| Isaac Sopoaga | 62 | 20 | 11 | 0.0 | 1 |
| Ricky Jean Francois | 30 | 12 | 3 | 0.0 | 0 |
Interceptions
| Player | INT | INTYDS | INTLG | INTTD |
| Carlos Rogers | 6 | 106 | 31 | 1 |
| Dashon Goldson | 6 | 53 | 21 | 0 |
| Tarell Brown | 4 | 15 | 11 | 0 |
| Donte Whitner | 2 | 48 | 48 | 0 |
| Tramaine Brock | 2 | 18 | 18 | 0 |
| Patrick Willis | 1 | 10 | 10 | 0 |
| Chris Culliver | 1 | 23 | 23 | 0 |
| Tavares Gooden | 0 | 0 | 0 | 0 |
| Ray McDonald | 0 | 0 | 0 | 0 |
| Delanie Walker | 0 | 0 | 0 | 0 |
| Demarcus Dobbs | 0 | 0 | 0 | 0 |
| Will Tukuafu | 0 | 0 | 0 | 0 |
| C.J. Spillman | 0 | 0 | 0 | 0 |
| Bruce Davis | 0 | 0 | 0 | 0 |
| Ahmad Brooks | 0 | 0 | 0 | 0 |
| Aldon Smith | 0 | 0 | 0 | 0 |
| Justin Smith | 0 | 0 | 0 | 0 |
| Navorro Bowman | 0 | 0 | 0 | 0 |
| Larry Grant | 0 | 0 | 0 | 0 |
| Parys Haralson | 0 | 0 | 0 | 0 |
| Isaac Sopoaga | 0 | 0 | 0 | 0 |
| Ricky Jean Francois | 0 | 0 | 0 | 0 |
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