Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
1993 players
Passing
| Steve Young | 462 | 314 | 4,023 | 29 | 16 | 8.7 |
| Steve Bono | 61 | 39 | 416 | 0 | 1 | 6.8 |
| John Taylor | 1 | 1 | 41 | 0 | 0 | 41.0 |
Rushing
| Ricky Watters | 208 | 950 | 10 | 4.6 |
| Steve Young | 69 | 407 | 2 | 5.9 |
| Marc Logan | 58 | 280 | 7 | 4.8 |
| Amp Lee | 72 | 230 | 1 | 3.2 |
| Tom Rathman | 19 | 80 | 3 | 4.2 |
| Dexter Carter | 10 | 72 | 1 | 7.2 |
| Jerry Rice | 3 | 69 | 1 | 23.0 |
| Adam Walker | 5 | 17 | 0 | 3.4 |
| John Taylor | 2 | 17 | 0 | 8.5 |
| Steve Bono | 12 | 14 | 1 | 1.2 |
| Klaus Wilmsmeyer | 2 | 0 | 0 | 0.0 |
| Bill Musgrave | 3 | -3 | 0 | -1.0 |
Receiving
| Jerry Rice | 154 | 98 | 1,503 | 15 | 9.8 |
| John Taylor | 74 | 56 | 940 | 5 | 12.7 |
| Brent Jones | 95 | 68 | 735 | 3 | 7.7 |
| Marc Logan | 48 | 37 | 348 | 0 | 7.2 |
| Ricky Watters | 45 | 31 | 326 | 1 | 7.2 |
| Jamie Williams | 20 | 16 | 132 | 1 | 6.6 |
| Nate Singleton | 14 | 8 | 126 | 1 | 9.0 |
| Amp Lee | 20 | 16 | 115 | 2 | 5.8 |
| Tom Rathman | 14 | 10 | 86 | 0 | 6.1 |
| Odessa Turner | 7 | 3 | 64 | 0 | 9.1 |
| Sanjay Beach | 10 | 5 | 59 | 1 | 5.9 |
| Dexter Carter | 9 | 3 | 40 | 0 | 4.4 |
| Adam Walker | 1 | 1 | 4 | 0 | 4.0 |
| Steve Young | 2 | 2 | 2 | 0 | 1.0 |
Defense
| Bill Romanowski | RLB | 104 | 104 | 3.0 | 0 | 2 |
| Tim McDonald | SS | 91 | 91 | 0.0 | 3 | 0 |
| Eric Davis | LCB | 69 | 69 | 0.0 | 4 | 1 |
| Merton Hanks | FS | 67 | 67 | 0.0 | 3 | 0 |
| Dana Stubblefield | LDT | 64 | 64 | 10.5 | 0 | 2 |
| Dennis Brown | LDE | 58 | 58 | 5.5 | 0 | 2 |
| John Johnson | LLB | 46 | 46 | 2.0 | 1 | 3 |
| Ted Washington | RDT | 41 | 41 | 3.0 | 0 | 0 |
| Michael McGruder | RCB | 37 | 37 | 0.0 | 5 | 0 |
| Dana Hall | FS | 28 | 28 | 0.0 | 0 | 0 |
| Martin Harrison | LB | 23 | 23 | 6.0 | 0 | 2 |
| Don Griffin | RCB | 22 | 22 | 0.0 | 3 | 0 |
| Mark Thomas | DE | 15 | 15 | 0.5 | 0 | 0 |
| Artie Smith | RDE | 15 | 15 | 1.5 | 0 | 0 |
| Troy Wilson | DE | 15 | 15 | 5.5 | 0 | 0 |
| Todd Kelly | LLB | 15 | 15 | 1.0 | 0 | 0 |
| Karl Wilson | DE | 12 | 12 | 3.0 | 0 | 0 |
| Alan Grant | DB | 8 | 8 | 0.0 | 1 | 0 |
| Antonio Goss | LB | 8 | 8 | 0.0 | 0 | 0 |
| Terry Hoage | DB | 5 | 5 | 0.0 | 0 | 0 |
| Adrian Hardy | DB | 3 | 3 | 0.0 | 0 | 0 |
| Matt LaBounty | DE | 2 | 2 | 0.0 | 0 | 0 |
| Kevin Fagan | RDE | 0 | 0 | 1.0 | 0 | 1 |
| Larry Roberts | DE | 0 | 0 | 1.5 | 0 | 0 |