Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2016 players
Passing
| Colin Kaepernick | 331 | 196 | 2,241 | 16 | 4 | 6.8 |
| Blaine Gabbert | 160 | 91 | 925 | 5 | 6 | 5.8 |
Rushing
| Carlos Hyde | 217 | 988 | 6 | 4.6 |
| Colin Kaepernick | 69 | 468 | 2 | 6.8 |
| Shaun Draughn | 74 | 196 | 4 | 2.6 |
| Blaine Gabbert | 40 | 173 | 2 | 4.3 |
| DuJuan Harris | 38 | 138 | 0 | 3.6 |
| Mike Davis | 19 | 50 | 1 | 2.6 |
| Raheem Mostert | 1 | 6 | 0 | 6.0 |
Receiving
| Jeremy Kerley | 115 | 64 | 667 | 3 | 5.8 |
| Quinton Patton | 63 | 37 | 408 | 0 | 6.5 |
| Vance McDonald | 45 | 24 | 391 | 4 | 8.7 |
| Garrett Celek | 50 | 29 | 350 | 3 | 7.0 |
| Torrey Smith | 49 | 20 | 267 | 3 | 5.4 |
| Shaun Draughn | 39 | 29 | 263 | 2 | 6.7 |
| Rod Streater | 27 | 18 | 191 | 2 | 7.1 |
| Carlos Hyde | 33 | 27 | 163 | 3 | 4.9 |
| Chris Harper | 21 | 13 | 133 | 0 | 6.3 |
| DuJuan Harris | 9 | 8 | 115 | 1 | 12.8 |
| Aaron Burbridge | 16 | 7 | 88 | 0 | 5.5 |
| Blake Bell | 9 | 4 | 85 | 0 | 9.4 |
| Mike Davis | 5 | 3 | 25 | 0 | 5.0 |
| DeAndre Smelter | 1 | 1 | 23 | 0 | 23.0 |
| Je'Ron Hamm | 4 | 2 | 13 | 0 | 3.2 |
| Blaine Gabbert | 1 | 1 | -16 | 0 | -16.0 |