Franchise 77 seasons 563–571–9 all-time 20 playoff trips 1 Super Bowls
1990 players
Passing
| Jim Harbaugh | 312 | 180 | 2,178 | 10 | 6 | 7.0 |
| Mike Tomczak | 104 | 39 | 521 | 3 | 5 | 5.0 |
| Peter Tom Willis | 13 | 9 | 106 | 1 | 1 | 8.2 |
| Johnny Bailey | 1 | 1 | 22 | 0 | 0 | 22.0 |
Rushing
| Neal Anderson | 260 | 1,078 | 10 | 4.1 |
| Brad Muster | 141 | 664 | 6 | 4.7 |
| Jim Harbaugh | 51 | 321 | 4 | 6.3 |
| Mark Green | 27 | 126 | 0 | 4.7 |
| Johnny Bailey | 26 | 86 | 0 | 3.3 |
| James Rouse | 16 | 56 | 0 | 3.5 |
| Dennis Gentry | 11 | 43 | 0 | 3.9 |
| Mike Tomczak | 12 | 41 | 2 | 3.4 |
| Ron Morris | 2 | 26 | 0 | 13.0 |
| Lars Tate | 3 | 5 | 0 | 1.7 |
| William Perry | 1 | -1 | 0 | -1.0 |
| Maury Buford | 1 | -9 | 0 | -9.0 |
Receiving
| Wendell Davis | 73 | 39 | 572 | 3 | 7.8 |
| Neal Anderson | 59 | 42 | 484 | 3 | 8.2 |
| Brad Muster | 68 | 47 | 452 | 0 | 6.6 |
| Ron Morris | 70 | 31 | 437 | 3 | 6.2 |
| Dennis Gentry | 41 | 23 | 320 | 2 | 7.8 |
| James Thornton | 49 | 19 | 254 | 1 | 5.2 |
| Cap Boso | 14 | 11 | 135 | 1 | 9.6 |
| Glen Kozlowski | 17 | 7 | 83 | 0 | 4.9 |
| Tom Waddle | 6 | 2 | 32 | 0 | 5.3 |
| Mark Green | 7 | 4 | 26 | 1 | 3.7 |
| Quintin Smith | 3 | 2 | 20 | 0 | 6.7 |
| James Coley | 2 | 1 | 7 | 0 | 3.5 |
| Mike Tomczak | 1 | 1 | 5 | 0 | 5.0 |
Defense
| Shaun Gayle | SS | 125 | 125 | 1.0 | 2 | 2 |
| Mark Carrier | FS | 122 | 122 | 0.0 | 10 | 5 |
| Trace Armstrong | LDE | 82 | 82 | 10.0 | 0 | 2 |
| Richard Dent | RDE | 81 | 81 | 12.0 | 3 | 2 |
| Steve McMichael | RDT | 71 | 71 | 4.0 | 0 | 0 |
| William Perry | LDT | 70 | 70 | 4.0 | 0 | 2 |
| Donnell Woolford | LCB | 70 | 70 | 2.0 | 3 | 0 |
| David Tate | DB | 54 | 54 | 0.0 | 0 | 0 |
| Ron Cox | LB | 28 | 28 | 3.0 | 0 | 1 |
| John Mangum | DB | 13 | 13 | 0.0 | 0 | 1 |
| Dante Jones | LB | 9 | 9 | 2.0 | 0 | 0 |
| Glenell Sanders | LB | 2 | 2 | 0.0 | 0 | 0 |
| Maurice Douglass | DB | 1 | 1 | 0.0 | 0 | 0 |
| Mickey Pruitt | LB | 0 | 0 | 1.0 | 0 | 1 |
| John Roper | LB | 0 | 0 | 1.0 | 0 | 0 |
| Mike Singletary | MLB | 0 | 0 | 1.0 | 0 | 1 |