Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
1989 players
Passing
| Joe Montana | 386 | 271 | 3,521 | 26 | 8 | 9.1 |
| Steve Young | 92 | 64 | 1,001 | 8 | 3 | 10.9 |
| Steve Bono | 5 | 4 | 62 | 1 | 0 | 12.4 |
Rushing
| Roger Craig | 271 | 1,054 | 6 | 3.9 |
| Tom Rathman | 79 | 305 | 1 | 3.9 |
| Joe Montana | 49 | 227 | 3 | 4.6 |
| Terrence Flagler | 33 | 129 | 1 | 3.9 |
| Steve Young | 38 | 126 | 2 | 3.3 |
| Harry Sydney | 9 | 56 | 0 | 6.2 |
| Jerry Rice | 5 | 33 | 0 | 6.6 |
| Keith Henderson | 7 | 30 | 1 | 4.3 |
| John Taylor | 1 | 6 | 0 | 6.0 |
| Barry Helton | 1 | 0 | 0 | 0.0 |
Receiving
| Jerry Rice | 131 | 82 | 1,483 | 17 | 11.3 |
| John Taylor | 76 | 60 | 1,077 | 10 | 14.2 |
| Tom Rathman | 86 | 73 | 616 | 1 | 7.2 |
| Brent Jones | 57 | 40 | 500 | 4 | 8.8 |
| Roger Craig | 67 | 49 | 473 | 1 | 7.1 |
| Keith Henderson | 5 | 3 | 130 | 0 | 26.0 |
| Mike Wilson | 23 | 9 | 103 | 1 | 4.5 |
| Harry Sydney | 10 | 9 | 71 | 0 | 7.1 |
| Terrence Flagler | 7 | 6 | 51 | 0 | 7.3 |
| Jamie Williams | 3 | 3 | 38 | 0 | 12.7 |
| Terry Greer | 2 | 1 | 26 | 0 | 13.0 |
| Wesley Walls | 8 | 4 | 16 | 1 | 2.0 |
Defense
| Charles Haley | LOLB | 57 | 57 | 10.5 | 0 | 5 |
| Bill Romanowski | LB | 53 | 53 | 1.0 | 1 | 1 |
| Pierce Holt | LDE | 48 | 48 | 10.5 | 0 | 1 |
| Don Griffin | RCB | 47 | 47 | 0.0 | 2 | 1 |
| Ronnie Lott | FS | 42 | 42 | 0.0 | 5 | 0 |
| Danny Stubbs | DE | 13 | 13 | 4.5 | 0 | 1 |
| Tim McKyer | DB | 12 | 12 | 0.0 | 1 | 0 |
| Antonio Goss | LB | 5 | 5 | 0.0 | 0 | 0 |
| Kevin Fagan | RDE | 0 | 0 | 7.0 | 0 | 2 |
| Larry Roberts | LDE | 0 | 0 | 3.5 | 0 | 1 |
| Mike Walter | RILB | 0 | 0 | 1.0 | 0 | 1 |
| Chet Brooks | SS | 0 | 0 | 1.0 | 3 | 1 |
| Pete Kugler | NT | 0 | 0 | 3.0 | 0 | 0 |