Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
1999 players
Passing
| Jeff Garcia | 375 | 225 | 2,544 | 11 | 11 | 6.8 |
| Steve Stenstrom | 100 | 54 | 536 | 0 | 4 | 5.4 |
| Steve Young | 84 | 45 | 446 | 3 | 4 | 5.3 |
| Jerry Rice | 1 | 0 | 0 | 0 | 0 | 0.0 |
Rushing
| Charlie Garner | 241 | 1,229 | 4 | 5.1 |
| Fred Beasley | 58 | 276 | 4 | 4.8 |
| Jeff Garcia | 45 | 231 | 2 | 5.1 |
| Lawrence Phillips | 30 | 144 | 2 | 4.8 |
| Terry Jackson | 15 | 75 | 0 | 5.0 |
| Steve Young | 11 | 57 | 0 | 5.2 |
| Travis Jervey | 6 | 49 | 1 | 8.2 |
| Steve Stenstrom | 3 | 15 | 0 | 5.0 |
| Jerry Rice | 2 | 13 | 0 | 6.5 |
| Tommy Vardell | 6 | 6 | 1 | 1.0 |
| Chad Stanley | 1 | 0 | 0 | 0.0 |
Receiving
| Jerry Rice | 124 | 67 | 830 | 5 | 6.7 |
| Terrell Owens | 98 | 60 | 754 | 4 | 7.7 |
| Charlie Garner | 76 | 56 | 535 | 2 | 7.0 |
| J.J. Stokes | 79 | 34 | 429 | 3 | 5.4 |
| Greg Clark | 55 | 34 | 347 | 0 | 6.3 |
| Fred Beasley | 51 | 32 | 282 | 0 | 5.5 |
| Lawrence Phillips | 20 | 15 | 152 | 0 | 7.6 |
| Mark Harris | 14 | 6 | 66 | 0 | 4.7 |
| Tony Cline | 5 | 4 | 45 | 0 | 9.0 |
| Tommy Vardell | 11 | 7 | 36 | 0 | 3.3 |
| Tai Streets | 3 | 2 | 25 | 0 | 8.3 |
| Steve Stenstrom | 1 | 1 | 9 | 0 | 9.0 |
| Chad Fann | 8 | 2 | 8 | 0 | 1.0 |
| Terry Jackson | 3 | 3 | 6 | 0 | 2.0 |
| Travis Jervey | 1 | 1 | 2 | 0 | 2.0 |
Defense
| Ken Norton Jr. | RLB | 100 | 74 | 1.0 | 0 | 7 | 1 |
| Ken Norton Jr. | RLB | 100 | 74 | 1.0 | 0 | 7 | 1 |
| Winfred Tubbs | MLB | 88 | 74 | 2.0 | 1 | 3 | 0 |
| Tim McDonald | SS | 69 | 52 | 2.0 | 2 | 4 | 1 |
| Lee Woodall | LLB | 68 | 54 | 2.5 | 0 | 5 | 1 |
| Lance Schulters | FS | 64 | 55 | 0.0 | 6 | 9 | 0 |
| Junior Bryant | RDT/LDE | 48 | 39 | 4.5 | 0 | 6 | 2 |
| Darnell Walker | LCB | 47 | 43 | 1.0 | 1 | 4 | 1 |
| Ramos McDonald | LCB | 44 | 42 | 0.0 | 1 | 11 | 0 |
| Brentson Buckner | RDT | 44 | 29 | 1.0 | 0 | 4 | 0 |
| Pierson Prioleau | RCB | 44 | 35 | 0.0 | 0 | 10 | 1 |
| Bryant Young | LDT | 41 | 36 | 11.0 | 0 | 5 | 0 |
| R.W. McQuarters | DB | 29 | 26 | 0.0 | 1 | 5 | 0 |
| Zack Bronson | DB | 28 | 20 | 0.0 | 0 | 1 | 0 |
| Gabe Wilkins | RDE | 26 | 17 | 1.0 | 0 | 1 | 0 |
| Jeff Posey | LDE | 21 | 16 | 2.0 | 0 | 2 | 0 |
| Chike Okeafor | DE | 20 | 18 | 1.0 | 0 | 1 | 1 |
| Craig Newsome | DB | 16 | 13 | 0.0 | 0 | 0 | 0 |
| 13 | 13 | 5.0 | 0 | 0 | 4 | ||
| Reggie Givens | LB | 12 | 11 | 0.0 | 0 | 0 | 0 |
| Wasswa Serwanga | DB | 11 | 10 | 0.0 | 0 | 1 | 0 |
| Charles Haley | DE | 10 | 9 | 3.0 | 0 | 3 | 0 |
| Marvin Washington | LDE | 10 | 8 | 0.0 | 0 | 2 | 0 |
| Tony Peterson | LB | 8 | 6 | 0.0 | 0 | 1 | 0 |
| Chris Draft | LB | 5 | 4 | 0.0 | 0 | 0 | 0 |
| Derrick Deese | OT | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Joe Wesley | LB | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Matt Keneley | DT | 3 | 1 | 0.0 | 0 | 0 | 0 |
| Shonn Bell | TE | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Dave Fiore | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Chris Dalman | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Shane Bonham | DT | 1 | 1 | 0.0 | 0 | 0 | 0 |
| David Richie | NT | 1 | 0 | 0.0 | 0 | 0 | 0 |
| Phil Ostrowski | G | 1 | 1 | 0.0 | 0 | 0 | 0 |