Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2020 players
Passing
| Nick Mullens | 326 | 211 | 2,437 | 12 | 12 | 7.5 |
| Jimmy Garoppolo | 140 | 94 | 1,096 | 7 | 5 | 7.8 |
| C.J. Beathard | 104 | 66 | 787 | 6 | 0 | 7.6 |
Rushing
| Jeff Wilson | 126 | 600 | 7 | 4.8 |
| Raheem Mostert | 104 | 521 | 2 | 5.0 |
| Jerick McKinnon | 81 | 319 | 5 | 3.9 |
| JaMycal Hasty | 39 | 148 | 1 | 3.8 |
| Brandon Aiyuk | 6 | 77 | 2 | 12.8 |
| Kyle Juszczyk | 17 | 64 | 2 | 3.8 |
| Tevin Coleman | 28 | 53 | 0 | 1.9 |
| C.J. Beathard | 6 | 28 | 0 | 4.7 |
| Deebo Samuel Sr. | 8 | 26 | 0 | 3.2 |
| Jimmy Garoppolo | 10 | 25 | 0 | 2.5 |
| George Kittle | 2 | 17 | 0 | 8.5 |
| Nick Mullens | 9 | 8 | 0 | 0.9 |
| Austin Walter | 1 | 3 | 0 | 3.0 |
Receiving
| Brandon Aiyuk | 96 | 60 | 748 | 5 | 7.8 |
| Kendrick Bourne | 74 | 49 | 667 | 2 | 9.0 |
| George Kittle | 63 | 48 | 634 | 2 | 10.1 |
| Richie James | 35 | 23 | 394 | 1 | 11.3 |
| Deebo Samuel Sr. | 44 | 33 | 391 | 1 | 8.9 |
| Jerick McKinnon | 46 | 33 | 253 | 1 | 5.5 |
| Ross Dwelley | 24 | 19 | 245 | 1 | 10.2 |
| Jordan Reed | 46 | 26 | 231 | 4 | 5.0 |
| Kyle Juszczyk | 29 | 19 | 202 | 4 | 7.0 |
| Raheem Mostert | 19 | 16 | 156 | 1 | 8.2 |
| Jeff Wilson | 28 | 13 | 133 | 3 | 4.8 |
| Trent Taylor | 21 | 10 | 86 | 0 | 4.1 |
| River Cracraft | 9 | 6 | 41 | 0 | 4.6 |
| Charlie Woerner | 4 | 3 | 36 | 0 | 9.0 |
| Tevin Coleman | 5 | 4 | 34 | 0 | 6.8 |
| JaMycal Hasty | 8 | 7 | 33 | 0 | 4.1 |
| Austin Walter | 1 | 1 | 27 | 0 | 27.0 |