Franchise 76 seasons 584–547–10 all-time 29 playoff trips 2 Super Bowls
1996 players
Passing
| Jim Harbaugh | 405 | 232 | 2,630 | 13 | 11 | 6.5 |
| Paul Justin | 127 | 74 | 839 | 2 | 0 | 6.6 |
| Kerwin Bell | 5 | 5 | 75 | 1 | 0 | 15.0 |
Rushing
| Marshall Faulk | 198 | 587 | 7 | 3.0 |
| Lamont Warren | 67 | 230 | 1 | 3.4 |
| Jim Harbaugh | 48 | 192 | 1 | 4.0 |
| Clif Groce | 46 | 184 | 0 | 4.0 |
| Zack Crockett | 31 | 164 | 0 | 5.3 |
| Vince Workman | 24 | 70 | 0 | 2.9 |
| Marvin Harrison | 3 | 15 | 0 | 5.0 |
| Paul Justin | 2 | 7 | 0 | 3.5 |
| Kerwin Bell | 1 | -1 | 0 | -1.0 |
Receiving
| Marvin Harrison | 118 | 64 | 836 | 8 | 7.1 |
| Sean Dawkins | 91 | 54 | 751 | 1 | 8.3 |
| Ken Dilger | 60 | 42 | 503 | 4 | 8.4 |
| Marshall Faulk | 80 | 56 | 428 | 0 | 5.4 |
| Aaron Bailey | 36 | 18 | 302 | 0 | 8.4 |
| Brian Stablein | 34 | 18 | 192 | 1 | 5.6 |
| Lamont Warren | 35 | 22 | 174 | 0 | 5.0 |
| Clif Groce | 32 | 13 | 106 | 0 | 3.3 |
| Zack Crockett | 15 | 11 | 96 | 1 | 6.4 |
| Marcus Pollard | 12 | 6 | 86 | 1 | 7.2 |
| Vince Workman | 4 | 4 | 36 | 0 | 9.0 |
| Mark Stock | 4 | 2 | 24 | 0 | 6.0 |
| Chris Doering | 1 | 1 | 10 | 0 | 10.0 |
Defense
| Jason Belser | FS | 96 | 74 | 1.0 | 4 | 2 |
| Jeff Herrod | MLB | 72 | 53 | 0.0 | 1 | 0 |
| Steve Grant | LLB | 67 | 50 | 1.0 | 0 | 0 |
| Bernard Whittington | LDE | 66 | 46 | 3.0 | 0 | 2 |
| Tony Bennett | RDE | 65 | 43 | 6.0 | 0 | 3 |
| Ray Buchanan | LCB | 62 | 53 | 0.5 | 2 | 0 |
| Dedric Mathis | RCB | 51 | 43 | 0.0 | 0 | 0 |
| Tony McCoy | LDT | 50 | 36 | 5.0 | 0 | 0 |
| Steve Morrison | RLB | 48 | 38 | 0.0 | 1 | 0 |
| David Tate | SS | 47 | 28 | 1.0 | 0 | 1 |
| Tony Siragusa | RDT | 45 | 36 | 2.0 | 0 | 0 |
| Sammie Burroughs | LB | 42 | 32 | 0.0 | 0 | 3 |
| Quentin Coryatt | RLB | 40 | 32 | 0.0 | 0 | 0 |
| Ray McElroy | SS | 39 | 30 | 0.0 | 0 | 0 |
| Eugene Daniel | RCB | 36 | 31 | 0.0 | 3 | 1 |
| Steve Martin | RDT | 36 | 25 | 1.0 | 0 | 0 |
| Trev Alberts | LB | 27 | 19 | 0.0 | 1 | 1 |
| Elijah Alexander | LB | 26 | 22 | 1.0 | 0 | 0 |
| Ellis Johnson | LDE | 22 | 14 | 0.0 | 0 | 0 |
| Richard Dent | DE | 15 | 13 | 6.5 | 0 | 2 |
| Derrick Frazier | DB | 13 | 11 | 0.0 | 0 | 0 |
| Derwin Gray | DB | 6 | 3 | 0.0 | 0 | 0 |
| Richard Jones | DB | 5 | 5 | 0.0 | 0 | 0 |
| Damon Watts | DB | 5 | 3 | 0.0 | 1 | 0 |