Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2006 players
Passing
| Alex Smith | 443 | 259 | 2,901 | 16 | 15 | 6.5 |
| Arnaz Battle | 1 | 0 | 0 | 0 | 0 | 0.0 |
| Michael Robinson | 1 | 0 | 0 | 0 | 0 | 0.0 |
Rushing
| Frank Gore | 313 | 1,695 | 8 | 5.4 |
| Alex Smith | 41 | 151 | 2 | 3.7 |
| Michael Robinson | 38 | 116 | 2 | 3.1 |
| Bryan Gilmore | 7 | 94 | 0 | 13.4 |
| Maurice Hicks | 29 | 82 | 0 | 2.8 |
| Arnaz Battle | 4 | 28 | 0 | 7.0 |
| Moran Norris | 2 | 8 | 0 | 4.0 |
| Vernon Davis | 2 | 5 | 0 | 2.5 |
Receiving
| Antonio Bryant | 41 | 747 | 3 | 18.2 |
| Arnaz Battle | 60 | 683 | 3 | 11.4 |
| Frank Gore | 61 | 485 | 1 | 8.0 |
| Eric Johnson | 34 | 292 | 2 | 8.6 |
| Vernon Davis | 20 | 265 | 3 | 13.2 |
| Bryan Gilmore | 8 | 150 | 1 | 18.8 |
| Maurice Hicks | 13 | 137 | 1 | 10.5 |
| Michael Robinson | 9 | 47 | 0 | 5.2 |
| Moran Norris | 5 | 36 | 2 | 7.2 |
| Delanie Walker | 2 | 30 | 0 | 15.0 |
| Taylor Jacobs | 4 | 29 | 0 | 7.2 |
| Chris Hetherington | 2 | 0 | 0 | 0.0 |
Defense
| Brandon Moore | LB | 83 | 53 | 6.5 | 0 | 2 | 2 |
| Keith Lewis | DB | 72 | 55 | 1.0 | 2 | 4 | 1 |
| Walt Harris | CB | 62 | 51 | 1.0 | 8 | 20 | 4 |
| Mike Adams | FS | 62 | 51 | 0.0 | 0 | 3 | 0 |
| Derek M. Smith | ILB | 61 | 42 | 0.5 | 0 | 0 | 1 |
| Jeff Ulbrich | ILB | 56 | 38 | 0.0 | 0 | 0 | 0 |
| Shawntae Spencer | CB | 55 | 47 | 2.0 | 1 | 9 | 2 |
| Marques Douglas | DT | 53 | 39 | 3.0 | 0 | 1 | 2 |
| Mark Roman | S | 52 | 40 | 1.0 | 1 | 7 | 1 |
| Manny Lawson | OLB | 48 | 39 | 3.0 | 1 | 2 | 0 |
| Bryant Young | DT | 46 | 36 | 5.0 | 0 | 1 | 1 |
| Melvin Oliver | DE | 35 | 27 | 1.0 | 0 | 0 | 0 |
| Chad Williams | DB | 28 | 24 | 2.5 | 1 | 1 | 0 |
| Sammy Davis | DB | 27 | 20 | 0.0 | 0 | 7 | 0 |
| Ronald Fields | DT | 21 | 13 | 0.0 | 0 | 1 | 0 |
| Isaac Sopoaga | NT | 21 | 17 | 1.0 | 0 | 3 | 1 |
| Anthony Adams | DT | 19 | 11 | 2.0 | 0 | 1 | 0 |
| Hannibal Navies | LB | 16 | 10 | 0.0 | 0 | 0 | 0 |
| Maurice Hicks | RB | 15 | 12 | 0.0 | 0 | 0 | 0 |
| Marcus Hudson | SAF | 14 | 11 | 0.0 | 0 | 1 | 1 |
| T.J. Slaughter | LB | 13 | 8 | 0.0 | 0 | 0 | 0 |
| Michael Robinson | FB | 13 | 11 | 0.0 | 0 | 0 | 0 |
| Roderick Green | LB | 10 | 6 | 4.5 | 0 | 0 | 0 |
| Brian Jennings | LS | 6 | 4 | 0.0 | 0 | 0 | 1 |
| Bryan Gilmore | WR | 5 | 4 | 0.0 | 0 | 0 | 0 |
| Antonio Bryant | WR | 5 | 5 | 0.0 | 0 | 0 | 0 |
| Justin Smiley | G | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Moran Norris | FB | 3 | 1 | 0.0 | 0 | 0 | 0 |
| Frank Gore | RB | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Donald Strickland | DB | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Parys Haralson | OLB | 3 | 3 | 0.0 | 0 | 0 | 0 |
| B.J. Tucker | DB | 3 | 3 | 0.0 | 0 | 1 | 0 |
| Eric Heitmann | C | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Damane Duckett | OT | 3 | 2 | 0.0 | 0 | 1 | 0 |
| Arnaz Battle | WR | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Alex Smith | QB | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Renauld Williams | LB | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Joe Nedney | K | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Andy Lee | P | 2 | 1 | 0.0 | 0 | 0 | 0 |
| Jonas Jennings | OT | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Larry Allen | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Deke Cooper | FS | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Kwame Harris | OT | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Tony Wragge | C | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Vernon Davis | TE | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Billy Bajema | TE | 1 | 0 | 0.0 | 0 | 0 | 0 |