Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
1986 players
Passing
| Joe Montana | 307 | 191 | 2,236 | 8 | 9 | 7.3 |
| Jeff Kemp | 200 | 119 | 1,554 | 11 | 8 | 7.8 |
| Mike Moroski | 73 | 42 | 493 | 2 | 3 | 6.8 |
| Jerry Rice | 2 | 1 | 16 | 0 | 0 | 8.0 |
Rushing
| Roger Craig | 204 | 830 | 7 | 4.1 |
| Joe Cribbs | 152 | 590 | 5 | 3.9 |
| Tom Rathman | 33 | 138 | 1 | 4.2 |
| Wendell Tyler | 31 | 127 | 0 | 4.1 |
| Derrick Harmon | 27 | 77 | 1 | 2.9 |
| Jerry Rice | 10 | 72 | 1 | 7.2 |
| Jeff Kemp | 15 | 49 | 0 | 3.3 |
| Tony Cherry | 11 | 42 | 0 | 3.8 |
| Joe Montana | 17 | 38 | 0 | 2.2 |
| Mike Moroski | 6 | 22 | 1 | 3.7 |
| Bill Ring | 3 | 4 | 0 | 1.3 |
| John Frank | 1 | -3 | 0 | -3.0 |
Receiving
| Jerry Rice | 152 | 86 | 1,570 | 15 | 10.3 |
| Dwight Clark | 109 | 61 | 794 | 2 | 7.3 |
| Roger Craig | 103 | 81 | 624 | 0 | 6.1 |
| Russ Francis | 60 | 41 | 505 | 1 | 8.4 |
| Joe Cribbs | 55 | 35 | 346 | 0 | 6.3 |
| Tom Rathman | 15 | 13 | 121 | 0 | 8.1 |
| Mike Wilson | 21 | 9 | 104 | 1 | 5.0 |
| Derrick Harmon | 10 | 8 | 78 | 0 | 7.8 |
| Derrick Crawford | 10 | 5 | 70 | 0 | 7.0 |
| John Frank | 19 | 9 | 61 | 2 | 3.2 |
| Ken Margerum | 4 | 2 | 12 | 0 | 3.0 |
| Bill Ring | 1 | 1 | 8 | 0 | 8.0 |
| Carl Monroe | 3 | 2 | 6 | 0 | 2.0 |
Defense
| Ronnie Lott | FS | 77 | 77 | 2.0 | 10 | 0 |
| Don Griffin | RCB | 72 | 72 | 1.0 | 3 | 1 |
| Charles Haley | LB | 59 | 59 | 12.0 | 1 | 3 |
| Tim McKyer | LCB | 52 | 52 | 0.0 | 6 | 0 |
| Larry Roberts | DE | 0 | 0 | 5.5 | 0 | 1 |
| Mike Walter | LB | 0 | 0 | 1.0 | 0 | 1 |
| Dwaine Board | RDE | 0 | 0 | 8.0 | 0 | 1 |
| Michael Carter | NT | 0 | 0 | 2.0 | 0 | 0 |
| Jim Fahnhorst | RILB | 0 | 0 | 1.0 | 4 | 0 |
| Jeff Fuller | DB | 0 | 0 | 2.5 | 4 | 0 |
| Dennis Harrison | DE | 0 | 0 | 1.0 | 0 | 0 |
| Milt McColl | LOLB | 0 | 0 | 2.0 | 0 | 0 |
| Jeff Stover | LDE | 0 | 0 | 11.0 | 0 | 0 |
| Keena Turner | ROLB | 0 | 0 | 3.0 | 1 | 3 |