Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
1990 players
Passing
| Joe Montana | 520 | 321 | 3,944 | 26 | 16 | 7.6 |
| Steve Young | 62 | 38 | 427 | 2 | 0 | 6.9 |
| Barry Helton | 1 | 1 | 0 | 0 | 0 | 0.0 |
Rushing
| Dexter Carter | 114 | 460 | 1 | 4.0 |
| Roger Craig | 141 | 439 | 1 | 3.1 |
| Tom Rathman | 101 | 318 | 7 | 3.1 |
| Harry Sydney | 35 | 166 | 2 | 4.7 |
| Joe Montana | 40 | 162 | 1 | 4.0 |
| Steve Young | 15 | 159 | 0 | 10.6 |
| Keith Henderson | 6 | 14 | 0 | 2.3 |
| Jerry Rice | 2 | 0 | 0 | 0.0 |
Receiving
| Jerry Rice | 176 | 100 | 1,502 | 13 | 8.5 |
| John Taylor | 79 | 49 | 748 | 7 | 9.5 |
| Brent Jones | 80 | 56 | 747 | 5 | 9.3 |
| Tom Rathman | 68 | 48 | 327 | 0 | 4.8 |
| Mike Sherrard | 31 | 17 | 264 | 2 | 8.5 |
| Dexter Carter | 31 | 25 | 217 | 0 | 7.0 |
| Roger Craig | 39 | 25 | 201 | 0 | 5.2 |
| Harry Sydney | 15 | 10 | 116 | 1 | 7.7 |
| Mike Wilson | 19 | 7 | 89 | 0 | 4.7 |
| Jamie Williams | 12 | 9 | 54 | 0 | 4.5 |
| Ron Lewis | 5 | 5 | 44 | 0 | 8.8 |
| Keith Henderson | 5 | 4 | 35 | 0 | 7.0 |
| Wesley Walls | 12 | 5 | 27 | 0 | 2.2 |
Defense
| Bill Romanowski | ROLB | 79 | 79 | 1.0 | 0 | 0 |
| Charles Haley | LOLB | 58 | 58 | 16.0 | 0 | 5 |
| Ronnie Lott | FS | 53 | 53 | 0.0 | 3 | 1 |
| Pierce Holt | LDE | 51 | 51 | 5.5 | 0 | 0 |
| Don Griffin | RCB | 35 | 35 | 0.0 | 3 | 1 |
| Eric Davis | DB | 21 | 21 | 0.0 | 1 | 1 |
| Dennis Brown | DE | 9 | 9 | 6.0 | 0 | 0 |
| Martin Harrison | LB | 4 | 4 | 0.0 | 0 | 0 |
| Kevin Fagan | RDE | 0 | 0 | 9.5 | 0 | 1 |
| Jim Burt | NT | 0 | 0 | 2.0 | 0 | 0 |
| Johnnie Jackson | DB | 0 | 0 | 1.0 | 0 | 2 |
| Larry Roberts | DE | 0 | 0 | 1.0 | 0 | 0 |
| Michael Carter | NT | 0 | 0 | 1.0 | 0 | 0 |
| Keena Turner | LB | 0 | 0 | 1.0 | 0 | 0 |