Franchise 58 seasons 473–417–7 all-time 23 playoff trips 3 Super Bowls
2013 players
Passing
| Alex Smith | 508 | 308 | 3,313 | 23 | 7 | 6.5 |
| Chase Daniel | 38 | 25 | 248 | 1 | 1 | 6.5 |
Rushing
| Jamaal Charles | 259 | 1,287 | 12 | 5.0 |
| Alex Smith | 76 | 431 | 1 | 5.7 |
| Knile Davis | 70 | 242 | 4 | 3.5 |
| Chase Daniel | 14 | 52 | 0 | 3.7 |
| Cyrus Gray | 9 | 24 | 0 | 2.7 |
| A.J. Jenkins | 2 | 6 | 0 | 3.0 |
| Donnie Avery | 2 | 6 | 0 | 3.0 |
| Dexter McCluster | 8 | 5 | 0 | 0.6 |
| Anthony Sherman | 2 | 3 | 0 | 1.5 |
Receiving
| Jamaal Charles | 104 | 70 | 693 | 7 | 6.7 |
| Dwayne Bowe | 103 | 57 | 673 | 5 | 6.5 |
| Donnie Avery | 72 | 40 | 596 | 2 | 8.3 |
| Dexter McCluster | 83 | 53 | 511 | 2 | 6.2 |
| Sean McGrath | 40 | 26 | 302 | 2 | 7.6 |
| Anthony Fasano | 33 | 23 | 200 | 3 | 6.1 |
| Anthony Sherman | 24 | 18 | 155 | 1 | 6.5 |
| A.J. Jenkins | 17 | 8 | 130 | 0 | 7.6 |
| Junior Hemingway | 19 | 13 | 125 | 2 | 6.6 |
| Knile Davis | 15 | 11 | 75 | 0 | 5.0 |
| Cyrus Gray | 10 | 7 | 46 | 0 | 4.6 |
| Kevin Brock | 6 | 3 | 36 | 0 | 6.0 |
| Chad Hall | 7 | 2 | 20 | 0 | 2.9 |
| Richard Gordon | 1 | 1 | 3 | 0 | 3.0 |
| Alex Smith | 1 | 1 | -4 | 0 | -4.0 |
Defense
| Derrick Johnson | LB | 107 | 95 | 4.5 | 2 | 6 | 0 |
| Eric Berry | DB | 70 | 62 | 3.5 | 3 | 11 | 1 |
| Brandon Flowers | CB | 67 | 62 | 1.0 | 1 | 8 | 0 |
| Akeem Jordan | ILB | 66 | 53 | 0.0 | 0 | 0 | 2 |
| Kendrick Lewis | S | 54 | 44 | 0.0 | 1 | 4 | 0 |
| Dontari Poe | DT | 48 | 40 | 4.5 | 0 | 4 | 0 |
| Sean Smith | CB | 47 | 43 | 0.0 | 2 | 13 | 0 |
| Tamba Hali | OLB | 44 | 37 | 11.0 | 1 | 1 | 4 |
| Justin Houston | OLB | 43 | 40 | 11.0 | 0 | 4 | 1 |
| Marcus Cooper | DB | 42 | 39 | 0.0 | 3 | 18 | 1 |
| Quintin Demps | S | 34 | 23 | 0.0 | 4 | 9 | 0 |
| Tyson Jackson | DE | 33 | 24 | 4.0 | 0 | 3 | 0 |
| Allen Bailey | DE | 29 | 24 | 1.0 | 0 | 2 | 0 |
| Mike DeVito | DE | 27 | 17 | 0.0 | 0 | 1 | 0 |
| Frank Zombo | LB | 26 | 22 | 2.0 | 1 | 2 | 1 |
| Husain Abdullah | FS | 25 | 20 | 0.5 | 1 | 4 | 0 |
| Ron Parker | FS | 16 | 16 | 1.0 | 2 | 3 | 1 |
| James-Michael Johnson | LB | 14 | 14 | 1.0 | 0 | 1 | 1 |
| Dunta Robinson | CB | 13 | 13 | 0.0 | 0 | 4 | 0 |
| Josh Martin | LB | 11 | 10 | 0.0 | 0 | 0 | 1 |
| Junior Hemingway | WR | 10 | 8 | 0.0 | 0 | 0 | 0 |
| Anthony Sherman | FB | 10 | 9 | 0.0 | 0 | 0 | 0 |
| Cyrus Gray | RB | 7 | 6 | 0.0 | 0 | 0 | 0 |
| Nico Johnson | LB | 7 | 5 | 0.0 | 0 | 0 | 0 |
| Anthony Toribio | DT | 5 | 3 | 0.0 | 0 | 0 | 0 |
| Dezman Moses | LB | 5 | 3 | 0.0 | 0 | 0 | 0 |
| Jaye Howard | DE | 5 | 4 | 0.0 | 0 | 0 | 0 |
| Mike Catapano | OLB | 4 | 3 | 1.0 | 0 | 0 | 0 |
| Jamaal Charles | RB | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Thomas Gafford | LS | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Jerrell Powe | NT | 2 | 1 | 1.0 | 0 | 1 | 0 |
| Geoff Schwartz | G | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Dwayne Bowe | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Dustin Colquitt | P | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Alex Smith | QB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Dexter McCluster | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Jon Asamoah | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Rodney Hudson | C | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Ryan Succop | K | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Sean McGrath | TE | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Jeff Allen | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Knile Davis | RB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Sanders Commings | CB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Eric Fisher | OT | 1 | 1 | 0.0 | 0 | 0 | 0 |