Franchise 76 seasons 584–547–10 all-time 29 playoff trips 2 Super Bowls
1997 players
Passing
| Jim Harbaugh | 309 | 189 | 2,060 | 10 | 4 | 6.7 |
| Paul Justin | 140 | 83 | 1,046 | 5 | 5 | 7.5 |
| Kelly Holcomb | 73 | 45 | 454 | 1 | 8 | 6.2 |
| Lamont Warren | 1 | 0 | 0 | 0 | 0 | 0.0 |
Rushing
| Marshall Faulk | 264 | 1,054 | 7 | 4.0 |
| Zack Crockett | 95 | 300 | 1 | 3.2 |
| Jim Harbaugh | 36 | 206 | 0 | 5.7 |
| Lamont Warren | 28 | 80 | 2 | 2.9 |
| Clif Groce | 10 | 66 | 0 | 6.6 |
| Aaron Bailey | 3 | 20 | 0 | 6.7 |
| Kelly Holcomb | 5 | 5 | 0 | 1.0 |
| Paul Justin | 6 | 2 | 0 | 0.3 |
| Marvin Harrison | 2 | -7 | 0 | -3.5 |
Receiving
| Marvin Harrison | 118 | 73 | 866 | 6 | 7.3 |
| Sean Dawkins | 111 | 68 | 804 | 2 | 7.2 |
| Marshall Faulk | 73 | 47 | 471 | 1 | 6.5 |
| Ken Dilger | 36 | 27 | 380 | 3 | 10.6 |
| Aaron Bailey | 56 | 26 | 329 | 3 | 5.9 |
| Brian Stablein | 31 | 25 | 253 | 1 | 8.2 |
| Lamont Warren | 26 | 20 | 192 | 0 | 7.4 |
| Marcus Pollard | 19 | 10 | 116 | 0 | 6.1 |
| Zack Crockett | 24 | 15 | 112 | 0 | 4.7 |
| Scott Slutzker | 7 | 3 | 22 | 0 | 3.1 |
| Chris Doering | 2 | 2 | 12 | 0 | 6.0 |
| Tarik Glenn | 1 | 1 | 3 | 0 | 3.0 |
Defense
| Jason Belser | FS | 94 | 67 | 1.0 | 2 | 2 |
| Quentin Coryatt | RLB | 80 | 59 | 2.0 | 2 | 2 |
| Elijah Alexander | LLB | 66 | 52 | 1.0 | 1 | 1 |
| Robert Blackmon | SS | 65 | 48 | 3.0 | 1 | 1 |
| Ellis Johnson | RDT | 56 | 38 | 4.5 | 1 | 1 |
| Tony McCoy | LDT | 53 | 35 | 2.5 | 0 | 0 |
| Albert Fontenot | LDE | 46 | 22 | 4.5 | 0 | 2 |
| Bernard Whittington | LDT | 45 | 35 | 0.0 | 0 | 0 |
| Dan Footman | RDE | 44 | 36 | 10.5 | 0 | 1 |
| Steve Grant | MLB | 44 | 29 | 0.0 | 0 | 0 |
| Steve Morrison | LLB | 39 | 22 | 1.0 | 1 | 0 |
| Dedric Mathis | RCB | 34 | 27 | 0.0 | 1 | 0 |
| Ray McElroy | DB | 33 | 24 | 0.0 | 0 | 1 |
| Sammie Burroughs | LB | 29 | 20 | 1.0 | 0 | 0 |
| Carlton Gray | LCB | 24 | 20 | 0.0 | 2 | 0 |
| Damon Watts | RCB | 24 | 17 | 0.0 | 0 | 0 |
| Monty Montgomery | DB | 23 | 19 | 1.0 | 0 | 1 |
| Tony Bennett | RDE | 17 | 14 | 3.0 | 0 | 2 |
| Scott Von der Ahe | LB | 16 | 14 | 0.0 | 0 | 0 |
| Steve Martin | DT | 16 | 9 | 0.0 | 0 | 0 |
| Derwin Gray | DB | 9 | 4 | 0.0 | 0 | 0 |
| David Tate | DB | 9 | 6 | 0.0 | 0 | 0 |
| Rico Clark | DB | 8 | 7 | 0.0 | 1 | 0 |
| Kendel Shello | DE | 4 | 3 | 1.0 | 0 | 0 |
| Carl Powell | DE | 3 | 3 | 0.0 | 0 | 0 |