Franchise 77 seasons 609–519–14 all-time 30 playoff trips 5 Super Bowls
2007 players
Passing
| Trent Dilfer | 219 | 113 | 1,166 | 7 | 12 | 5.3 |
| Alex Smith | 193 | 94 | 914 | 2 | 4 | 4.7 |
| Shaun Hill | 80 | 54 | 501 | 5 | 2 | 6.3 |
| Chris Weinke | 22 | 13 | 104 | 1 | 0 | 4.7 |
Rushing
| Frank Gore | 260 | 1,102 | 5 | 4.2 |
| Michael Robinson | 26 | 121 | 0 | 4.7 |
| Maurice Hicks | 21 | 117 | 1 | 5.6 |
| Alex Smith | 13 | 89 | 0 | 6.8 |
| Trent Dilfer | 10 | 25 | 0 | 2.5 |
| Moran Norris | 7 | 17 | 0 | 2.4 |
| Shaun Hill | 12 | 14 | 1 | 1.2 |
| Arnaz Battle | 4 | 4 | 1 | 1.0 |
| Zak Keasey | 2 | 4 | 0 | 2.0 |
| Bryan Gilmore | 1 | -8 | 0 | -8.0 |
Receiving
| Arnaz Battle | 0 | 50 | 600 | 5 | 600.0 |
| Vernon Davis | 0 | 52 | 509 | 4 | 509.0 |
| Darrell Jackson | 1 | 46 | 497 | 3 | 497.0 |
| Frank Gore | 0 | 53 | 436 | 1 | 436.0 |
| Delanie Walker | 0 | 21 | 174 | 1 | 174.0 |
| Ashley Lelie | 0 | 10 | 115 | 0 | 115.0 |
| Bryan Gilmore | 0 | 7 | 111 | 0 | 111.0 |
| Maurice Hicks | 0 | 14 | 86 | 0 | 86.0 |
| Michael Robinson | 0 | 11 | 73 | 0 | 73.0 |
| Moran Norris | 0 | 6 | 38 | 0 | 38.0 |
| Jason Hill | 0 | 1 | 6 | 0 | 6.0 |
Defense
| Patrick Willis | ILB | 159 | 122 | 4.5 | 0 | 5 | 2 |
| Michael Lewis | S | 97 | 67 | 1.5 | 2 | 5 | 1 |
| Nate Clements | S | 86 | 71 | 1.0 | 4 | 14 | 3 |
| Derek M. Smith | ILB | 73 | 45 | 0.0 | 1 | 4 | 0 |
| Mark Roman | S | 60 | 45 | 0.0 | 0 | 4 | 0 |
| Marques Douglas | DT | 59 | 43 | 3.0 | 0 | 3 | 0 |
| Walt Harris | CB | 57 | 46 | 0.0 | 4 | 13 | 1 |
| Tully Banta-Cain | OLB | 39 | 28 | 3.5 | 0 | 2 | 0 |
| Parys Haralson | OLB | 37 | 23 | 2.0 | 0 | 0 | 0 |
| Jeff Ulbrich | ILB | 35 | 25 | 0.0 | 0 | 1 | 0 |
| Donald Strickland | DB | 32 | 22 | 0.0 | 0 | 5 | 0 |
| Bryant Young | DT | 30 | 26 | 5.5 | 0 | 2 | 1 |
| Shawntae Spencer | CB | 28 | 25 | 0.0 | 1 | 3 | 0 |
| Marcus Hudson | SAF | 24 | 17 | 0.0 | 0 | 2 | 0 |
| Aubrayo Franklin | NT | 22 | 14 | 0.0 | 0 | 1 | 1 |
| Brandon Moore | LB | 21 | 12 | 2.5 | 0 | 1 | 0 |
| Ronald Fields | DT | 21 | 11 | 1.0 | 0 | 0 | 1 |
| Isaac Sopoaga | NT | 18 | 11 | 1.5 | 0 | 1 | 0 |
| Keith Lewis | DB | 18 | 13 | 0.0 | 0 | 0 | 0 |
| Dashon Goldson | DB | 12 | 9 | 0.0 | 0 | 2 | 1 |
| Manny Lawson | OLB | 10 | 7 | 1.0 | 0 | 1 | 0 |
| Michael Robinson | FB | 10 | 8 | 0.0 | 0 | 0 | 0 |
| Hannibal Navies | LB | 9 | 5 | 1.0 | 0 | 0 | 1 |
| Maurice Hicks | RB | 9 | 4 | 0.0 | 0 | 0 | 0 |
| Zak Keasey | FB | 7 | 5 | 0.0 | 0 | 0 | 0 |
| Brian Jennings | LS | 5 | 3 | 0.0 | 0 | 0 | 0 |
| Michael L. Lewis | WR | 5 | 5 | 0.0 | 0 | 0 | 0 |
| Bryan Gilmore | WR | 5 | 3 | 0.0 | 0 | 0 | 0 |
| Roderick Green | LB | 4 | 4 | 2.0 | 0 | 0 | 0 |
| Trent Dilfer | QB | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Delanie Walker | TE | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Ray McDonald | DE | 3 | 3 | 1.0 | 0 | 0 | 0 |
| Moran Norris | FB | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Frank Gore | RB | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Tarell Brown | CB | 2 | 1 | 0.0 | 0 | 0 | 0 |
| Joe Nedney | K | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Joe Staley | OT | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Jason Hill | WR | 2 | 1 | 0.0 | 0 | 0 | 0 |
| Vernon Davis | TE | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Billy Bajema | TE | 2 | 1 | 0.0 | 0 | 0 | 0 |
| Larry Allen | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Darrell Jackson | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Alex Smith | QB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| David Baas | C | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Arnaz Battle | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Eric Heitmann | C | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Shaun Hill | QB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Justin Smiley | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Adam Snyder | G | 1 | 1 | 0.0 | 0 | 0 | 0 |