Franchise 58 seasons 473–417–7 all-time 23 playoff trips 3 Super Bowls
1994 players
Passing
| Joe Montana | 493 | 299 | 3,283 | 16 | 9 | 6.7 |
| Steve Bono | 117 | 66 | 796 | 4 | 4 | 6.8 |
| Matt Blundin | 5 | 1 | 13 | 0 | 1 | 2.6 |
Rushing
| Marcus Allen | 189 | 709 | 7 | 3.8 |
| Greg Hill | 141 | 574 | 1 | 4.1 |
| Kimble Anders | 62 | 231 | 2 | 3.7 |
| Donnell Bennett | 46 | 178 | 2 | 3.9 |
| Lake Dawson | 3 | 24 | 0 | 8.0 |
| Joe Montana | 18 | 17 | 0 | 0.9 |
| Ron Dickerson | 1 | 0 | 0 | 0.0 |
| Steve Bono | 4 | -1 | 0 | -0.2 |
Receiving
| Willie Davis | 98 | 51 | 822 | 5 | 8.4 |
| J.J. Birden | 91 | 48 | 637 | 4 | 7.0 |
| Lake Dawson | 68 | 37 | 537 | 2 | 7.9 |
| Kimble Anders | 93 | 67 | 525 | 1 | 5.6 |
| Derrick Walker | 51 | 36 | 382 | 2 | 7.5 |
| Marcus Allen | 60 | 42 | 349 | 0 | 5.8 |
| Eric Martin | 32 | 21 | 307 | 1 | 9.6 |
| Keith Cash | 29 | 19 | 192 | 2 | 6.6 |
| Greg Hill | 22 | 16 | 92 | 0 | 4.2 |
| Danan Hughes | 17 | 7 | 80 | 0 | 4.7 |
| Tracy Greene | 12 | 6 | 69 | 1 | 5.8 |
| Donnell Bennett | 11 | 7 | 53 | 0 | 4.8 |
| Chris Penn | 7 | 3 | 24 | 0 | 3.4 |
| Ron Dickerson | 2 | 2 | 11 | 0 | 5.5 |
| Jimmie Johnson | 5 | 2 | 7 | 0 | 1.4 |
| Joe Valerio | 2 | 2 | 5 | 2 | 2.5 |
Defense
| Dave Whitmore | SS | 79 | 48 | 0.0 | 0 | 1 |
| Tracy Simien | MLB | 72 | 58 | 0.0 | 0 | 0 |
| Derrick Thomas | RLB | 71 | 65 | 11.0 | 0 | 5 |
| George Jamison | LLB | 65 | 56 | 1.0 | 0 | 2 |
| William White | FS | 60 | 47 | 0.0 | 2 | 0 |
| Mark Collins | LCB | 56 | 50 | 2.0 | 2 | 0 |
| Neil Smith | LDE | 46 | 42 | 11.5 | 1 | 6 |
| Charles Mincy | SS | 45 | 39 | 0.0 | 3 | 0 |
| Joe Phillips | LDT | 40 | 38 | 3.0 | 0 | 1 |
| Darren Mickell | RDE | 38 | 35 | 7.0 | 0 | 4 |
| Jay Taylor | DB | 38 | 33 | 0.0 | 1 | 1 |
| Tracy Rogers | LB | 37 | 32 | 0.0 | 0 | 1 |
| Dan Saleaumua | RDT | 28 | 23 | 1.0 | 0 | 0 |
| Jaime Fields | LB | 16 | 15 | 0.0 | 0 | 2 |
| Vaughn Booker | DE | 15 | 13 | 0.0 | 0 | 1 |
| Doug Terry | DB | 13 | 8 | 0.0 | 0 | 0 |
| Pellom McDaniels | DE | 12 | 11 | 2.0 | 0 | 0 |
| Darren Anderson | DB | 10 | 9 | 0.0 | 0 | 0 |
| Greg Kragen | DT | 10 | 8 | 0.0 | 0 | 0 |
| Monty Grow | DB | 8 | 7 | 0.0 | 1 | 2 |
| Greg Manusky | LB | 8 | 6 | 0.0 | 0 | 0 |
| Bracy Walker | DB | 2 | 1 | 0.0 | 0 | 0 |
| Jerrol Williams | LB | 2 | 1 | 0.5 | 0 | 0 |
| Rob Waldrop | DT | 1 | 1 | 0.0 | 0 | 1 |