Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2013 players
Passing
| Colin Kaepernick | 416 | 243 | 3,197 | 21 | 8 | 7.7 |
| Colt McCoy | 1 | 1 | 13 | 0 | 0 | 13.0 |
Rushing
| Frank Gore | 276 | 1,128 | 9 | 4.1 |
| Colin Kaepernick | 92 | 524 | 4 | 5.7 |
| Kendall Hunter | 78 | 358 | 3 | 4.6 |
| LaMichael James | 12 | 59 | 0 | 4.9 |
| Anthony Dixon | 28 | 56 | 2 | 2.0 |
| Quinton Patton | 1 | 26 | 0 | 26.0 |
| Kyle Williams | 2 | 23 | 0 | 11.5 |
| Bruce Miller | 7 | 13 | 0 | 1.9 |
| Anquan Boldin | 2 | 11 | 0 | 5.5 |
| Colt McCoy | 6 | -6 | 0 | -1.0 |
Receiving
| Anquan Boldin | 129 | 85 | 1,179 | 7 | 9.1 |
| Vernon Davis | 84 | 52 | 850 | 13 | 10.1 |
| Michael Crabtree | 33 | 19 | 284 | 1 | 8.6 |
| Bruce Miller | 36 | 25 | 243 | 0 | 6.8 |
| Frank Gore | 26 | 16 | 141 | 0 | 5.4 |
| Vance McDonald | 19 | 8 | 119 | 0 | 6.3 |
| Kyle Williams | 27 | 12 | 113 | 0 | 4.2 |
| Mario Manningham | 23 | 9 | 85 | 0 | 3.7 |
| Garrett Celek | 4 | 2 | 38 | 0 | 9.5 |
| Quinton Patton | 5 | 3 | 34 | 0 | 6.8 |
| Anthony Dixon | 3 | 3 | 30 | 0 | 10.0 |
| Jon Baldwin | 9 | 3 | 28 | 0 | 3.1 |
| Kassim Osgood | 1 | 1 | 17 | 0 | 17.0 |
| LaMichael James | 3 | 2 | 16 | 0 | 5.3 |
| Joe Staley | 1 | 1 | 14 | 0 | 14.0 |
| Kendall Hunter | 4 | 2 | 13 | 0 | 3.2 |
Defense
| NaVorro Bowman | MLB | 128 | 103 | 5.0 | 2 | 8 | 4 |
| Patrick Willis | ILB | 97 | 75 | 3.0 | 0 | 1 | 2 |
| Eric Reid | S | 72 | 57 | 0.0 | 4 | 11 | 0 |
| Donte Whitner | S | 68 | 53 | 0.0 | 2 | 12 | 2 |
| Ahmad Brooks | OLB | 52 | 44 | 8.5 | 1 | 7 | 1 |
| Carlos Rogers | CB | 44 | 36 | 0.0 | 2 | 8 | 0 |
| Justin Smith | DE | 40 | 23 | 6.5 | 0 | 0 | 1 |
| Tramaine Brock | DB | 36 | 34 | 0.0 | 5 | 13 | 0 |
| Ray McDonald | DE | 33 | 25 | 3.5 | 0 | 1 | 0 |
| Tarell Brown | CB | 31 | 28 | 0.0 | 0 | 10 | 0 |
| Glenn Dorsey | NT | 31 | 18 | 2.0 | 0 | 0 | 0 |
| Michael Wilhoite | OLB | 31 | 29 | 0.0 | 0 | 1 | 0 |
| Aldon Smith | DE | 29 | 24 | 8.5 | 0 | 0 | 0 |
| C.J. Spillman | DB | 23 | 17 | 0.0 | 0 | 0 | 0 |
| Tony Jerod-Eddie | DE | 23 | 16 | 0.0 | 1 | 2 | 0 |
| Dan Skuta | OLB | 22 | 15 | 0.0 | 0 | 2 | 0 |
| Corey Lemonier | OLB | 15 | 12 | 1.0 | 0 | 2 | 1 |
| Demarcus Dobbs | DE | 13 | 5 | 0.0 | 0 | 1 | 0 |
| Craig Dahl | S | 13 | 9 | 0.0 | 0 | 0 | 0 |
| Raymond Ventrone | DB | 10 | 7 | 0.0 | 0 | 0 | 0 |
| Kassim Osgood | WR | 9 | 6 | 0.0 | 0 | 0 | 0 |
| Eric Wright | DB | 7 | 7 | 0.0 | 1 | 2 | 0 |
| Darryl Morris | DB | 6 | 4 | 0.0 | 0 | 0 | 0 |
| Bruce Miller | FB | 6 | 5 | 0.0 | 0 | 0 | 0 |
| Anthony Dixon | RB | 5 | 5 | 0.0 | 0 | 0 | 1 |
| Kendall Hunter | RB | 5 | 5 | 0.0 | 0 | 0 | 0 |
| Nick Moody | LB | 4 | 3 | 0.0 | 0 | 0 | 0 |
| Alex Boone | OT | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Anquan Boldin | WR | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Nnamdi Asomugha | CB | 2 | 2 | 0.0 | 0 | 1 | 0 |
| Mike Iupati | G | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Joe Staley | OT | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Ian Williams | NT | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Colin Kaepernick | QB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Quinton Dial | DT | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Vance McDonald | TE | 1 | 1 | 0.0 | 0 | 0 | 0 |