| Passing | G | Comp | Att | Pct | Yds | Y/A | Y/G | TD | Int | Long | Sack | Yds/L | QBRat | Fum | FumL |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Colin Kaepernick | 13 | 136 | 218 | 62.4 | 1814 | 8.3 | 139.5 | 10 | 3 | 57 | 16 | 112 | 98.3 | 9 | 2 |
| Alex Smith | 10 | 153 | 218 | 70.2 | 1737 | 8.0 | 173.7 | 13 | 5 | 55 | 24 | 137 | 104.1 | 4 | 1 |
| Rushing | G | Rush | Yds | Y/G | Avg | Long | TD | Fum | FumL |
|---|---|---|---|---|---|---|---|---|---|
| Frank Gore | 16 | 258 | 1214 | 75.9 | 4.7 | 37 | 8 | 2 | 1 |
| Colin Kaepernick | 13 | 63 | 415 | 31.9 | 6.6 | 50 | 5 | 9 | 2 |
| Kendall Hunter | 11 | 72 | 371 | 33.7 | 5.2 | 26 | 2 | 0 | 0 |
| Alex Smith | 10 | 31 | 132 | 13.2 | 4.3 | 24 | 0 | 4 | 1 |
| LaMichael James | 4 | 27 | 125 | 31.3 | 4.6 | 26 | 0 | 1 | 0 |
| Anthony Dixon | 16 | 21 | 78 | 4.9 | 3.7 | 9 | 2 | 0 | 0 |
| Mario Manningham | 12 | 3 | 64 | 5.3 | 21.3 | 29 | 0 | 2 | 1 |
| Dashon Goldson | 16 | 1 | 31 | 1.9 | 31.0 | 31 | 0 | 0 | 0 |
| Kyle Williams | 11 | 4 | 21 | 1.9 | 5.3 | 9 | 0 | 1 | 0 |
| Bruce Miller | 16 | 5 | 18 | 1.1 | 3.6 | 9 | 0 | 0 | 0 |
| Michael Crabtree | 16 | 1 | 8 | 0.5 | 8.0 | 8 | 0 | 0 | 0 |
| Brandon Jacobs | 2 | 5 | 7 | 3.5 | 1.4 | 3 | 0 | 0 | 0 |
| Ted Ginn Jr. | 13 | 1 | 7 | 0.5 | 7.0 | 7 | 0 | 0 | 0 |
| Receiving | G | Rec | Yds | Y/G | Avg | Long | YAC | 1stD | TD | Fum | FumL |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Michael Crabtree | 16 | 85 | 1105 | 69.1 | 13.0 | 49 | 544 | 57 | 9 | 0 | 0 |
| Vernon Davis | 16 | 41 | 548 | 34.3 | 13.4 | 53 | 172 | 26 | 5 | 0 | 0 |
| Mario Manningham | 12 | 42 | 449 | 37.4 | 10.7 | 40 | 181 | 21 | 1 | 2 | 1 |
| Randy Moss | 16 | 28 | 434 | 27.1 | 15.5 | 55 | 82 | 22 | 3 | 1 | 0 |
| Delanie Walker | 16 | 21 | 344 | 21.5 | 16.4 | 45 | 57 | 14 | 3 | 1 | 1 |
| Frank Gore | 16 | 28 | 234 | 14.6 | 8.4 | 26 | 233 | 10 | 1 | 2 | 1 |
| Kyle Williams | 11 | 14 | 212 | 19.3 | 15.1 | 57 | 79 | 10 | 1 | 1 | 0 |
| Bruce Miller | 16 | 12 | 84 | 5.3 | 7.0 | 26 | 66 | 4 | 0 | 0 | 0 |
| Kendall Hunter | 11 | 9 | 60 | 5.5 | 6.7 | 12 | 59 | 3 | 0 | 0 | 0 |
| Garrett Celek | 13 | 4 | 51 | 3.9 | 12.8 | 35 | 24 | 2 | 0 | 0 | 0 |
| LaMichael James | 4 | 3 | 29 | 7.3 | 9.7 | 15 | 22 | 3 | 0 | 1 | 0 |
| Ted Ginn Jr. | 13 | 2 | 1 | 0.1 | 0.5 | 1 | 7 | 0 | 0 | 0 | 0 |
| Field Goals | PAT | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Kicking | G | 0-19 | 20-29 | 30-39 | 40-49 | 50+ | FGM | FGA | Pct | Long | XPM | XPA |
| David Akers | 16 | 1-1 | 8-9 | 11-13 | 7-13 | 2-6 | 29 | 42 | 64.9 | 63 | 44 | 44 |
| Kickoff Returns | Punt Returns | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Returns | G | KR | Yds | FC | Avg | Long | TD | PR | Yds | FC | Avg | Long | TD |
| LaMichael James | 4 | 14 | 417 | 0 | 29.8 | 62 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Kyle Williams | 11 | 13 | 353 | 0 | 27.2 | 94 | 0 | 4 | 52 | 6 | 13.0 | 20 | 0 |
| Ted Ginn Jr. | 13 | 11 | 253 | 0 | 23.0 | 31 | 0 | 32 | 326 | 12 | 10.2 | 38 | 0 |
| Kendall Hunter | 11 | 7 | 165 | 0 | 23.6 | 31 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Delanie Walker | 16 | 4 | 28 | 0 | 7.0 | 18 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Tackles | Interceptions | Misc. | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Defense | G | Solo | Ast | Total | Sack | YdsL | Int | Yds | IntTD | PD | Sfty |
| Ahmad Brooks | 16 | 35 | 12 | 47 | 6.5 | 50 | 1 | 50 | 1 | 6 | 0 |
| Donte Whitner | 16 | 61 | 21 | 82 | 0.0 | 0 | 1 | 42 | 1 | 5 | 0 |
| Will Tukuafu | 14 | 5 | 2 | 7 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Brian Jennings | 16 | 2 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Michael Wilhoite | 5 | 5 | 0 | 7 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Larry Grant | 16 | 6 | 0 | 6 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Perrish Cox | 16 | 17 | 2 | 20 | 0.0 | 0 | 0 | 0 | 0 | 2 | 0 |
| Bruce Miller | 16 | 9 | 0 | 11 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Carlos Rogers | 16 | 50 | 6 | 56 | 1.0 | 7 | 1 | 63 | 0 | 7 | 0 |
| Dashon Goldson | 16 | 55 | 14 | 69 | 0.0 | 0 | 3 | 21 | 0 | 11 | 0 |
| C.J. Spillman | 16 | 10 | 0 | 11 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Tramaine Brock | 16 | 14 | 0 | 16 | 0.0 | 0 | 0 | 0 | 0 | 1 | 0 |
| David Akers | 16 | 2 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Clark Haggans | 9 | 2 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Delanie Walker | 16 | 5 | 0 | 6 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Mario Manningham | 12 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NaVorro Bowman | 16 | 97 | 51 | 149 | 2.0 | 9 | 1 | 11 | 0 | 6 | 0 |
| Chris Culliver | 16 | 41 | 7 | 48 | 0.0 | 0 | 2 | 4 | 0 | 14 | 0 |
| Isaac Sopoaga | 15 | 21 | 6 | 27 | 1.0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Ray McDonald | 16 | 28 | 10 | 38 | 2.5 | 16 | 0 | 0 | 0 | 1 | 1 |
| Ricky Jean Francois | 16 | 12 | 10 | 22 | 2.0 | 16 | 0 | 0 | 0 | 0 | 0 |
| Kyle Williams | 11 | 2 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ted Ginn Jr. | 13 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Tavares Gooden | 15 | 7 | 0 | 9 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Mike Iupati | 16 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Aldon Smith | 16 | 50 | 16 | 66 | 19.5 | 145 | 1 | 6 | 0 | 1 | 0 |
| Justin Smith | 14 | 47 | 19 | 66 | 3.0 | 23 | 0 | 0 | 0 | 2 | 0 |
| Ian Williams | 3 | 3 | 0 | 3 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Patrick Willis | 16 | 88 | 32 | 120 | 0.5 | 5 | 2 | 2 | 0 | 9 | 0 |
| Darcel McBath | 16 | 4 | 0 | 7 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Anthony Dixon | 16 | 4 | 0 | 7 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Demarcus Dobbs | 12 | 3 | 2 | 5 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Vernon Davis | 16 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Tarell Brown | 16 | 50 | 5 | 55 | 0.0 | 0 | 2 | 17 | 0 | 14 | 0 |
| Anthony Davis | 16 | 2 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |