Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2008 players
Passing
| Shaun Hill | 288 | 181 | 2,046 | 13 | 8 | 7.1 |
| J.T. O'Sullivan | 220 | 128 | 1,678 | 8 | 11 | 7.6 |
| Isaac Bruce | 1 | 0 | 0 | 0 | 0 | 0.0 |
Rushing
| Frank Gore | 240 | 1,036 | 6 | 4.3 |
| DeShaun Foster | 76 | 234 | 1 | 3.1 |
| J.T. O'Sullivan | 30 | 145 | 0 | 4.8 |
| Shaun Hill | 24 | 115 | 2 | 4.8 |
| Michael Robinson | 19 | 50 | 0 | 2.6 |
| Arnaz Battle | 1 | 18 | 0 | 18.0 |
| Vernon Davis | 1 | 11 | 0 | 11.0 |
| Jason Hill | 2 | 5 | 0 | 2.5 |
| Allen Rossum | 1 | 1 | 1 | 1.0 |
| Isaac Bruce | 1 | -3 | 0 | -3.0 |
| Delanie Walker | 2 | -13 | 0 | -6.5 |
Receiving
| Isaac Bruce | 60 | 833 | 7 | 13.9 |
| Bryant Johnson | 45 | 546 | 3 | 12.1 |
| Frank Gore | 43 | 373 | 2 | 8.7 |
| Vernon Davis | 31 | 358 | 2 | 11.5 |
| Jason Hill | 31 | 319 | 2 | 10.3 |
| Josh Morgan | 20 | 319 | 3 | 16.0 |
| Arnaz Battle | 24 | 318 | 0 | 13.2 |
| Michael Robinson | 17 | 202 | 0 | 11.9 |
| Delanie Walker | 10 | 155 | 1 | 15.5 |
| DeShaun Foster | 16 | 133 | 1 | 8.3 |
| Dominique Zeigler | 5 | 97 | 0 | 19.4 |
| Billy Bajema | 2 | 34 | 0 | 17.0 |
| Zak Keasey | 3 | 25 | 0 | 8.3 |
| Sean Ryan | 3 | 15 | 0 | 5.0 |
| Allen Rossum | 1 | 4 | 0 | 4.0 |
Defense
| Patrick Willis | ILB | 120 | 88 | 1.0 | 1 | 10 | 1 |
| Takeo Spikes | ILB | 91 | 56 | 1.0 | 3 | 7 | 2 |
| Michael Lewis | S | 90 | 70 | 2.0 | 0 | 7 | 1 |
| Justin Smith | DE | 69 | 44 | 7.0 | 1 | 3 | 1 |
| Nate Clements | S | 57 | 50 | 0.0 | 2 | 9 | 1 |
| Walt Harris | CB | 53 | 43 | 1.0 | 3 | 14 | 0 |
| Mark Roman | S | 48 | 34 | 0.0 | 0 | 5 | 0 |
| Manny Lawson | OLB | 44 | 32 | 3.0 | 0 | 3 | 1 |
| Aubrayo Franklin | NT | 43 | 30 | 1.0 | 0 | 2 | 2 |
| Donald Strickland | DB | 38 | 28 | 0.0 | 0 | 5 | 1 |
| Parys Haralson | OLB | 38 | 26 | 8.5 | 0 | 2 | 0 |
| Isaac Sopoaga | NT | 37 | 23 | 1.0 | 0 | 1 | 0 |
| Tarell Brown | CB | 28 | 24 | 0.0 | 2 | 3 | 0 |
| Ray McDonald | DE | 26 | 19 | 1.0 | 0 | 4 | 0 |
| Dashon Goldson | DB | 18 | 15 | 0.0 | 0 | 1 | 0 |
| Keith Lewis | DB | 18 | 13 | 0.0 | 0 | 1 | 1 |
| Jeff Ulbrich | ILB | 17 | 13 | 0.0 | 0 | 0 | 0 |
| Ronald Fields | DT | 16 | 10 | 0.0 | 0 | 0 | 0 |
| Tully Banta-Cain | OLB | 16 | 10 | 0.5 | 0 | 0 | 0 |
| Delanie Walker | TE | 14 | 10 | 0.0 | 0 | 0 | 0 |
| Michael Robinson | FB | 10 | 8 | 0.0 | 0 | 0 | 0 |
| Roderick Green | LB | 10 | 5 | 3.0 | 0 | 1 | 0 |
| Jason Hill | WR | 8 | 6 | 0.0 | 0 | 0 | 0 |
| Marcus Hudson | SAF | 7 | 6 | 0.0 | 0 | 0 | 0 |
| Kentwan Balmer | DE | 7 | 6 | 0.0 | 0 | 1 | 0 |
| Zak Keasey | FB | 6 | 5 | 0.0 | 0 | 0 | 0 |
| Dominique Zeigler | WR | 5 | 5 | 0.0 | 0 | 0 | 0 |
| Billy Bajema | TE | 5 | 2 | 0.0 | 0 | 0 | 0 |
| Brian Jennings | LS | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Reggie Smith | DB | 4 | 3 | 0.0 | 0 | 0 | 0 |
| Vernon Davis | TE | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Joe Staley | OT | 4 | 3 | 0.0 | 0 | 0 | 0 |
| Josh Morgan | WR | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Joe Nedney | K | 3 | 3 | 0.0 | 0 | 0 | 0 |
| J.T. O'Sullivan | QB | 2 | 2 | 0.0 | 0 | 0 | 1 |
| Shawntae Spencer | CB | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Eric Heitmann | C | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Bryant Johnson | WR | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Frank Gore | RB | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Shaun Hill | QB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Isaac Bruce | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| DeShaun Foster | RB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Tony Wragge | C | 1 | 1 | 0.0 | 0 | 0 | 0 |
| David Baas | C | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Arnaz Battle | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |