Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2012 players
Passing
| Colin Kaepernick | 218 | 136 | 1,814 | 10 | 3 | 8.3 |
| Alex Smith | 218 | 153 | 1,737 | 13 | 5 | 8.0 |
Rushing
| Frank Gore | 258 | 1,214 | 8 | 4.7 |
| Colin Kaepernick | 63 | 415 | 5 | 6.6 |
| Kendall Hunter | 72 | 371 | 2 | 5.2 |
| Alex Smith | 31 | 132 | 0 | 4.3 |
| LaMichael James | 27 | 125 | 0 | 4.6 |
| Anthony Dixon | 21 | 78 | 2 | 3.7 |
| Mario Manningham | 3 | 64 | 0 | 21.3 |
| Dashon Goldson | 1 | 31 | 0 | 31.0 |
| Kyle Williams | 4 | 21 | 0 | 5.2 |
| Bruce Miller | 5 | 18 | 0 | 3.6 |
| Michael Crabtree | 1 | 8 | 0 | 8.0 |
| Ted Ginn | 1 | 7 | 0 | 7.0 |
| Brandon Jacobs | 5 | 7 | 0 | 1.4 |
Receiving
| Michael Crabtree | 126 | 85 | 1,105 | 9 | 8.8 |
| Vernon Davis | 61 | 41 | 548 | 5 | 9.0 |
| Mario Manningham | 57 | 42 | 449 | 1 | 7.9 |
| Randy Moss | 50 | 28 | 434 | 3 | 8.7 |
| Delanie Walker | 39 | 21 | 344 | 3 | 8.8 |
| Frank Gore | 36 | 28 | 234 | 1 | 6.5 |
| Kyle Williams | 22 | 14 | 212 | 1 | 9.6 |
| Bruce Miller | 13 | 12 | 84 | 0 | 6.5 |
| Kendall Hunter | 12 | 9 | 60 | 0 | 5.0 |
| Garrett Celek | 7 | 4 | 51 | 0 | 7.3 |
| LaMichael James | 5 | 3 | 29 | 0 | 5.8 |
| Ted Ginn | 2 | 2 | 1 | 0 | 0.5 |
Defense
| NaVorro Bowman | MLB | 134 | 82 | 2.0 | 1 | 7 | 1 |
| Patrick Willis | ILB | 113 | 81 | 0.5 | 2 | 9 | 2 |
| Donte Whitner | S | 78 | 57 | 0.0 | 1 | 4 | 2 |
| Aldon Smith | DE | 63 | 47 | 19.5 | 1 | 1 | 3 |
| Dashon Goldson | DB | 63 | 49 | 0.0 | 3 | 12 | 1 |
| Justin Smith | DE | 61 | 42 | 3.0 | 0 | 2 | 0 |
| Carlos Rogers | CB | 53 | 47 | 1.0 | 1 | 6 | 0 |
| Tarell Brown | CB | 51 | 46 | 0.0 | 2 | 13 | 0 |
| Chris Culliver | DB | 46 | 39 | 0.0 | 2 | 12 | 1 |
| Ahmad Brooks | OLB | 40 | 28 | 6.5 | 1 | 6 | 2 |
| Ray McDonald | DE | 35 | 25 | 2.5 | 0 | 1 | 1 |
| Isaac Sopoaga | NT | 25 | 19 | 1.0 | 0 | 0 | 0 |
| Ricky Jean Francois | DT | 21 | 11 | 2.0 | 0 | 0 | 0 |
| Perrish Cox | CB | 18 | 15 | 0.0 | 0 | 2 | 0 |
| Tramaine Brock | DB | 15 | 13 | 0.0 | 0 | 1 | 1 |
| C.J. Spillman | DB | 11 | 10 | 0.0 | 0 | 0 | 0 |
| Tavares Gooden | LB | 9 | 7 | 0.0 | 0 | 0 | 0 |
| Bruce Miller | FB | 8 | 6 | 0.0 | 0 | 0 | 0 |
| Will Tukuafu | FB | 7 | 5 | 0.0 | 0 | 0 | 0 |
| Michael Wilhoite | OLB | 7 | 5 | 0.0 | 0 | 0 | 0 |
| Darcel McBath | DB | 7 | 4 | 0.0 | 0 | 0 | 0 |
| Anthony Dixon | RB | 6 | 3 | 0.0 | 0 | 0 | 1 |
| Delanie Walker | TE | 6 | 5 | 0.0 | 0 | 0 | 0 |
| Demarcus Dobbs | DE | 5 | 3 | 0.0 | 0 | 0 | 0 |
| Larry Grant | LB | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Clark Haggans | LB | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Brian Jennings | LS | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Ian Williams | NT | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Kyle Williams | WR | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Anthony Davis | OT | 2 | 2 | 0.0 | 0 | 0 | 0 |
| David Akers | K | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Mario Manningham | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Ted Ginn | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Vernon Davis | TE | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Mike Iupati | G | 1 | 1 | 0.0 | 0 | 0 | 0 |