Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
1987 players
Passing
| Joe Montana | 398 | 266 | 3,054 | 31 | 13 | 7.7 |
| Steve Young | 69 | 37 | 570 | 10 | 0 | 8.3 |
| Bob Gagliano | 29 | 16 | 229 | 1 | 1 | 7.9 |
| Mark Stevens | 4 | 2 | 52 | 1 | 0 | 13.0 |
| Harry Sydney | 1 | 1 | 50 | 1 | 0 | 50.0 |
Rushing
| Roger Craig | 215 | 815 | 3 | 3.8 |
| Joe Cribbs | 70 | 300 | 1 | 4.3 |
| Tom Rathman | 62 | 257 | 1 | 4.1 |
| Steve Young | 26 | 190 | 1 | 7.3 |
| Joe Montana | 35 | 141 | 1 | 4.0 |
| Harry Sydney | 29 | 125 | 0 | 4.3 |
| Mike Varajon | 18 | 82 | 0 | 4.6 |
| Tony Cherry | 13 | 65 | 1 | 5.0 |
| Jerry Rice | 8 | 51 | 1 | 6.4 |
| Andre Hardy | 7 | 48 | 0 | 6.9 |
| Del Rodgers | 11 | 46 | 1 | 4.2 |
| Mark Stevens | 10 | 45 | 1 | 4.5 |
| Doug DuBose | 10 | 33 | 0 | 3.3 |
| Carl Monroe | 2 | 26 | 0 | 13.0 |
| Terrence Flagler | 6 | 11 | 0 | 1.8 |
| John Frank | 1 | 2 | 0 | 2.0 |
| Ed Blount | 1 | 0 | 0 | 0.0 |
Receiving
| Jerry Rice | 112 | 65 | 1,078 | 22 | 9.6 |
| Roger Craig | 85 | 66 | 492 | 1 | 5.8 |
| Mike Wilson | 50 | 29 | 450 | 5 | 9.0 |
| Tom Rathman | 39 | 30 | 329 | 3 | 8.4 |
| John Frank | 33 | 26 | 296 | 3 | 9.0 |
| Dwight Clark | 35 | 24 | 290 | 5 | 8.3 |
| Russ Francis | 28 | 22 | 202 | 0 | 7.2 |
| Ron Heller | 24 | 12 | 165 | 3 | 6.9 |
| John Taylor | 16 | 9 | 151 | 0 | 9.4 |
| Terry Greer | 9 | 6 | 111 | 1 | 12.3 |
| Joe Cribbs | 11 | 9 | 70 | 0 | 6.4 |
| Carl Monroe | 10 | 3 | 66 | 1 | 6.6 |
| Tony Gladney | 5 | 4 | 60 | 0 | 12.0 |
| Del Rodgers | 4 | 2 | 45 | 0 | 11.2 |
| Doug DuBose | 4 | 4 | 37 | 0 | 9.2 |
| Brent Jones | 3 | 2 | 35 | 0 | 11.7 |
| Terrence Flagler | 4 | 2 | 28 | 0 | 7.0 |
| Mike Varajon | 4 | 3 | 25 | 0 | 6.2 |
| Chris Dressel | 1 | 1 | 8 | 0 | 8.0 |
| Ken Margerum | 3 | 1 | 7 | 0 | 2.3 |
| Andre Hardy | 1 | 1 | 7 | 0 | 7.0 |
| Harry Sydney | 3 | 1 | 3 | 0 | 1.0 |
Defense
| Ronnie Lott | FS | 55 | 55 | 0.0 | 5 | 2 |
| Tim McKyer | LCB | 35 | 35 | 0.0 | 2 | 1 |
| Charles Haley | LB | 25 | 25 | 6.5 | 0 | 1 |
| Don Griffin | RCB | 23 | 23 | 0.0 | 5 | 0 |
| Kevin Fagan | DE | 0 | 0 | 2.0 | 0 | 0 |
| Larry Roberts | DE | 0 | 0 | 2.5 | 0 | 0 |
| Dwaine Board | RDE | 0 | 0 | 2.0 | 0 | 1 |
| Keith Browner | LB | 0 | 0 | 0.5 | 0 | 1 |
| Michael Carter | NT | 0 | 0 | 1.0 | 0 | 2 |
| Glen Collins | DE | 0 | 0 | 2.0 | 0 | 1 |
| Matt Courtney | DB | 0 | 0 | 1.0 | 1 | 0 |
| Jeff Fuller | SS | 0 | 0 | 2.0 | 0 | 4 |
| Clyde Glover | DT | 0 | 0 | 2.0 | 0 | 0 |
| Mark Korff | LB | 0 | 0 | 1.5 | 0 | 1 |
| Pete Kugler | LDE | 0 | 0 | 4.5 | 0 | 0 |
| Milt McColl | LOLB | 0 | 0 | 1.0 | 1 | 0 |
| Todd Shell | LB | 0 | 0 | 1.0 | 1 | 0 |
| Jeff Stover | LDE | 0 | 0 | 3.5 | 0 | 0 |
| Keena Turner | ROLB | 0 | 0 | 3.0 | 1 | 1 |