Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2009 players
Passing
| Alex Smith | 372 | 225 | 2,350 | 18 | 12 | 6.3 |
| Shaun Hill | 155 | 87 | 943 | 5 | 2 | 6.1 |
Rushing
| Frank Gore | 229 | 1,120 | 10 | 4.9 |
| Glen Coffee | 83 | 226 | 1 | 2.7 |
| Shaun Hill | 8 | 70 | 0 | 8.8 |
| Josh Morgan | 5 | 61 | 0 | 12.2 |
| Alex Smith | 24 | 51 | 0 | 2.1 |
| Moran Norris | 14 | 41 | 1 | 2.9 |
| Delanie Walker | 3 | 34 | 0 | 11.3 |
| Michael Robinson | 3 | 2 | 0 | 0.7 |
| Isaac Bruce | 1 | -8 | 0 | -8.0 |
Receiving
| Vernon Davis | 129 | 78 | 965 | 13 | 7.5 |
| Michael Crabtree | 86 | 48 | 625 | 2 | 7.3 |
| Josh Morgan | 81 | 52 | 527 | 3 | 6.5 |
| Frank Gore | 75 | 52 | 406 | 3 | 5.4 |
| Isaac Bruce | 49 | 21 | 264 | 0 | 5.4 |
| Delanie Walker | 33 | 21 | 233 | 0 | 7.1 |
| Jason Hill | 17 | 9 | 90 | 2 | 5.3 |
| Glen Coffee | 18 | 11 | 76 | 0 | 4.2 |
| Arnaz Battle | 5 | 5 | 40 | 0 | 8.0 |
| Moran Norris | 11 | 7 | 31 | 0 | 2.8 |
| Michael Robinson | 11 | 6 | 24 | 0 | 2.2 |
| Brandon Jones | 5 | 1 | 18 | 0 | 3.6 |
| Alex Smith | 1 | 1 | -6 | 0 | -6.0 |
Defense
| Patrick Willis | ILB | 136 | 98 | 4.0 | 3 | 8 | 3 |
| Dashon Goldson | DB | 89 | 71 | 3.0 | 4 | 6 | 3 |
| Michael Lewis | S | 82 | 71 | 1.0 | 1 | 2 | 2 |
| Takeo Spikes | ILB | 67 | 49 | 3.0 | 0 | 1 | 0 |
| Manny Lawson | OLB | 58 | 41 | 6.5 | 0 | 2 | 3 |
| Mark Roman | S | 51 | 44 | 1.0 | 1 | 2 | 1 |
| Shawntae Spencer | CB | 49 | 45 | 0.0 | 2 | 10 | 0 |
| Justin Smith | DE | 48 | 34 | 6.0 | 0 | 1 | 2 |
| Parys Haralson | OLB | 42 | 30 | 5.0 | 0 | 2 | 0 |
| Tarell Brown | CB | 36 | 30 | 0.0 | 2 | 8 | 0 |
| Aubrayo Franklin | NT | 35 | 24 | 2.0 | 1 | 3 | 0 |
| Nate Clements | S | 33 | 28 | 0.0 | 1 | 7 | 0 |
| Isaac Sopoaga | NT | 27 | 17 | 1.0 | 0 | 1 | 0 |
| Dre' Bly | CB | 27 | 24 | 1.0 | 3 | 13 | 1 |
| Ahmad Brooks | OLB | 20 | 19 | 6.0 | 0 | 2 | 4 |
| Matt Wilhelm | LB | 18 | 12 | 0.0 | 0 | 0 | 0 |
| Scott McKillop | LB | 17 | 13 | 0.0 | 0 | 0 | 0 |
| Marcus Hudson | SAF | 15 | 11 | 0.0 | 0 | 0 | 0 |
| Delanie Walker | TE | 13 | 10 | 0.0 | 0 | 0 | 0 |
| Demetric Evans | DE | 12 | 5 | 1.5 | 0 | 1 | 0 |
| Kentwan Balmer | DE | 12 | 5 | 0.0 | 0 | 0 | 0 |
| Michael Robinson | FB | 11 | 9 | 0.0 | 0 | 0 | 0 |
| Glen Coffee | RB | 10 | 7 | 0.0 | 0 | 0 | 0 |
| Ray McDonald | DE | 8 | 6 | 3.0 | 0 | 0 | 0 |
| Arnaz Battle | WR | 7 | 7 | 0.0 | 0 | 0 | 1 |
| Brian Jennings | LS | 6 | 3 | 0.0 | 0 | 0 | 0 |
| Brit Miller | FB | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Reggie Smith | DB | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Jason Hill | WR | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Adam Snyder | G | 4 | 4 | 0.0 | 0 | 0 | 1 |
| Michael Crabtree | WR | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Keith Smith | DB | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Curtis Taylor | DB | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Chilo Rachal | G | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Josh Morgan | WR | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Joe Nedney | K | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Diyral Briggs | LB | 2 | 0 | 0.0 | 0 | 0 | 0 |
| Jeff Ulbrich | ILB | 1 | 0 | 0.0 | 0 | 0 | 0 |
| Isaac Bruce | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Alex Smith | QB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Andy Lee | P | 1 | 0 | 0.0 | 0 | 0 | 0 |