Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2018 players
Passing
| Nick Mullens | 274 | 176 | 2,277 | 13 | 10 | 8.3 |
| C.J. Beathard | 169 | 102 | 1,252 | 8 | 7 | 7.4 |
| Jimmy Garoppolo | 89 | 53 | 718 | 5 | 3 | 8.1 |
Rushing
| Matt Breida | 153 | 814 | 3 | 5.3 |
| Alfred Morris | 111 | 428 | 2 | 3.9 |
| Jeff Wilson | 66 | 266 | 0 | 4.0 |
| Raheem Mostert | 34 | 261 | 1 | 7.7 |
| C.J. Beathard | 19 | 69 | 1 | 3.6 |
| Jimmy Garoppolo | 8 | 33 | 0 | 4.1 |
| Kyle Juszczyk | 8 | 30 | 0 | 3.8 |
| George Kittle | 1 | 10 | 0 | 10.0 |
| Marquise Goodwin | 4 | 9 | 0 | 2.2 |
| Dante Pettis | 1 | -2 | 0 | -2.0 |
| Nick Mullens | 18 | -16 | 0 | -0.9 |
Receiving
| George Kittle | 136 | 88 | 1,377 | 5 | 10.1 |
| Kendrick Bourne | 67 | 42 | 487 | 4 | 7.3 |
| Dante Pettis | 45 | 27 | 467 | 5 | 10.4 |
| Marquise Goodwin | 44 | 23 | 395 | 4 | 9.0 |
| Kyle Juszczyk | 41 | 30 | 324 | 1 | 7.9 |
| Pierre Garcon | 46 | 24 | 286 | 1 | 6.2 |
| Matt Breida | 31 | 27 | 261 | 2 | 8.4 |
| Trent Taylor | 40 | 26 | 215 | 1 | 5.4 |
| Richie James | 14 | 9 | 130 | 1 | 9.3 |
| Jeff Wilson | 15 | 12 | 98 | 0 | 6.5 |
| Garrett Celek | 8 | 5 | 90 | 2 | 11.2 |
| Alfred Morris | 13 | 8 | 73 | 0 | 5.6 |
| Raheem Mostert | 7 | 6 | 25 | 0 | 3.6 |
| Ross Dwelley | 2 | 2 | 14 | 0 | 7.0 |
| Joe Staley | 1 | 1 | -5 | 0 | -5.0 |
Defense
| Fred Warner | MLB | 109 | 70 | 0.0 | 0 | 6 | 1 |
| DeForest Buckner | DT | 59 | 36 | 12.0 | 0 | 3 | 0 |
| Elijah Lee | OLB | 54 | 43 | 1.0 | 0 | 2 | 1 |
| Arik Armstead | DT | 44 | 29 | 3.0 | 0 | 0 | 0 |
| K'Waun Williams | DB | 43 | 38 | 0.0 | 0 | 2 | 0 |
| Jaquiski Tartt | S | 38 | 28 | 0.0 | 1 | 2 | 0 |
| D.J. Reed | CB | 37 | 26 | 1.0 | 0 | 0 | 1 |
| Ahkello Witherspoon | CB | 37 | 30 | 0.0 | 0 | 4 | 0 |
| Richard Sherman | CB | 36 | 29 | 1.0 | 0 | 4 | 0 |
| Antone Exum | S | 34 | 28 | 1.0 | 1 | 7 | 1 |
| Ronald Blair | DE | 33 | 21 | 5.5 | 0 | 0 | 0 |
| Cassius Marsh | LB | 33 | 22 | 5.5 | 0 | 0 | 0 |
| Malcolm Smith | MLB | 31 | 18 | 0.0 | 0 | 1 | 0 |
| Marcell Harris | DB | 30 | 20 | 0.0 | 0 | 0 | 0 |
| Reuben Foster | OLB | 26 | 22 | 0.0 | 0 | 1 | 0 |
| Solomon Thomas | DE | 26 | 19 | 1.0 | 0 | 0 | 0 |
| Earl Mitchell | DT | 24 | 13 | 0.0 | 0 | 0 | 0 |
| Jimmie Ward | SAF | 24 | 19 | 0.0 | 0 | 0 | 1 |
| Mark Nzeocha | OLB | 21 | 16 | 1.0 | 0 | 1 | 1 |
| Tarvarius Moore | DB | 21 | 18 | 0.0 | 0 | 2 | 1 |
| Adrian Colbert | FS | 19 | 13 | 0.0 | 0 | 1 | 0 |
| D.J. Jones | DT | 15 | 9 | 0.0 | 0 | 0 | 0 |
| Greg Mabin | CB | 15 | 11 | 0.0 | 0 | 1 | 1 |
| Sheldon Day | DT | 9 | 7 | 2.0 | 0 | 2 | 0 |
| Tyvis Powell | DB | 6 | 6 | 0.0 | 0 | 0 | 1 |
| Raheem Mostert | RB | 6 | 6 | 0.0 | 0 | 0 | 0 |
| Brock Coyle | LB | 6 | 4 | 0.0 | 0 | 0 | 0 |
| Jullian Taylor | DT | 5 | 2 | 0.0 | 0 | 0 | 0 |
| Garrett Celek | TE | 5 | 5 | 0.0 | 0 | 0 | 0 |
| Dekoda Watson | LB | 5 | 3 | 2.0 | 0 | 0 | 1 |
| Pierre Garcon | WR | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Marquise Goodwin | WR | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Pita Taumoepenu | LB | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Joe Staley | OT | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Godwin Igwebuike | RB | 2 | 1 | 0.0 | 0 | 0 | 0 |
| Weston Richburg | C | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Kyle Juszczyk | FB | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Richie James | WR | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Matt Dayes | RB | 2 | 1 | 0.0 | 0 | 0 | 0 |
| George Kittle | TE | 2 | 2 | 0.0 | 0 | 0 | 0 |
| C.J. Beathard | QB | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Terence Garvin | LB | 1 | 0 | 0.0 | 0 | 0 | 0 |
| Matt Breida | RB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Kendrick Bourne | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Trent Taylor | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Cole Wick | TE | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Bradley Pinion | P | 1 | 1 | 0.0 | 0 | 0 | 0 |
| James Onwualu | LB | 1 | 1 | 0.0 | 0 | 0 | 1 |
| Jeff Wilson | RB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Mike McGlinchey | OT | 1 | 1 | 0.0 | 0 | 0 | 0 |