Franchise 57 seasons 427–465–5 all-time 17 playoff trips 0 Super Bowls
2000 players
Passing
| Ryan Leaf | 309 | 155 | 1,821 | 11 | 17 | 5.9 |
| Jim Harbaugh | 202 | 123 | 1,416 | 8 | 10 | 7.0 |
| Moses Moreno | 31 | 16 | 134 | 0 | 2 | 4.3 |
| Robert Chancey | 1 | 0 | 0 | 0 | 0 | 0.0 |
Rushing
| Terrell Fletcher | 114 | 380 | 3 | 3.3 |
| Jermaine Fazande | 119 | 368 | 2 | 3.1 |
| Robert Chancey | 38 | 133 | 2 | 3.5 |
| Ryan Leaf | 28 | 54 | 0 | 1.9 |
| Curtis Conway | 3 | 31 | 0 | 10.3 |
| Jim Harbaugh | 16 | 24 | 0 | 1.5 |
| Kenny Bynum | 3 | 9 | 0 | 3.0 |
| Fred McCrary | 7 | 8 | 0 | 1.1 |
| Ronney Jenkins | 8 | 6 | 0 | 0.8 |
| Moses Moreno | 1 | 0 | 0 | 0.0 |
Receiving
| Jeff Graham | 113 | 55 | 907 | 4 | 8.0 |
| Freddie Jones | 123 | 67 | 721 | 5 | 5.9 |
| Curtis Conway | 97 | 51 | 694 | 5 | 7.2 |
| Terrell Fletcher | 63 | 41 | 289 | 1 | 4.6 |
| Reggie Jones | 38 | 22 | 253 | 0 | 6.7 |
| Trevor Gaylor | 28 | 12 | 174 | 1 | 6.2 |
| Fred McCrary | 25 | 17 | 122 | 2 | 4.9 |
| Jermaine Fazande | 18 | 16 | 104 | 0 | 5.8 |
| Mikhael Ricks | 6 | 3 | 35 | 0 | 5.8 |
| Steve Heiden | 12 | 6 | 32 | 1 | 2.7 |
| Nate Jacquet | 3 | 1 | 25 | 0 | 8.3 |
| Reggie Davis | 1 | 1 | 8 | 0 | 8.0 |
| Robert Chancey | 2 | 1 | 6 | 0 | 3.0 |
| Ronney Jenkins | 2 | 1 | 1 | 0 | 0.5 |
Defense
| Rodney Harrison | S | 98 | 74 | 6.0 | 6 | 16 | 1 |
| Junior Seau | LB | 93 | 73 | 3.5 | 2 | 11 | 0 |
| Mike Dumas | FS | 61 | 52 | 1.0 | 0 | 4 | 0 |
| Orlando Ruff | LB | 56 | 42 | 0.0 | 1 | 5 | 0 |
| John Parrella | DT | 52 | 39 | 6.0 | 0 | 5 | 2 |
| DeRon Jenkins | CB | 51 | 46 | 0.0 | 1 | 5 | 0 |
| Gerald Dixon | OLB | 47 | 39 | 5.0 | 1 | 5 | 0 |
| Jamal Williams | NT | 44 | 37 | 1.0 | 0 | 1 | 1 |
| Rogers Beckett | S | 39 | 28 | 0.0 | 1 | 2 | 0 |
| Fakhir Brown | CB | 36 | 29 | 0.0 | 1 | 10 | 0 |
| Darren Mickell | DE | 29 | 28 | 6.0 | 0 | 1 | 2 |
| Darryll Lewis | CB | 28 | 26 | 1.0 | 1 | 2 | 1 |
| Albert Fontenot | DE | 22 | 16 | 4.0 | 0 | 1 | 0 |
| Tony Darden | CB | 18 | 16 | 0.0 | 0 | 0 | 0 |
| Steve Tovar | LB | 17 | 14 | 0.0 | 0 | 0 | 0 |
| Scott Turner | DB | 14 | 14 | 0.0 | 1 | 1 | 0 |
| Fred McCrary | RB | 13 | 13 | 0.0 | 0 | 0 | 0 |
| Shannon Taylor | LB | 12 | 11 | 0.0 | 0 | 0 | 0 |
| Adrian Dingle | DE | 12 | 10 | 2.5 | 0 | 2 | 0 |
| Reggie Rusk | SAF | 11 | 11 | 1.0 | 0 | 0 | 0 |
| Deon Humphrey | LB | 9 | 8 | 0.0 | 0 | 0 | 0 |
| Greg Jackson | DB | 9 | 9 | 0.0 | 0 | 0 | 0 |
| Steve Heiden | TE | 8 | 8 | 0.0 | 0 | 0 | 0 |
| Mike Mohring | DT | 8 | 7 | 0.0 | 0 | 0 | 0 |
| Tim Denton | CB | 6 | 5 | 0.0 | 0 | 1 | 0 |
| Reggie Jones | WR | 6 | 6 | 0.0 | 0 | 0 | 0 |
| Kenny Bynum | RB | 5 | 5 | 0.0 | 0 | 0 | 0 |
| Terrell Fletcher | RB | 5 | 5 | 0.0 | 0 | 0 | 0 |
| Armon Hatcher | DB | 4 | 4 | 0.0 | 0 | 0 | 0 |
| Ronney Jenkins | RB | 3 | 3 | 0.0 | 0 | 0 | 0 |
| Ben Coleman | G | 3 | 3 | 0.0 | 0 | 0 | 0 |
| John Reeves | LB | 3 | 2 | 0.0 | 0 | 0 | 0 |
| Neil Smith | DE | 2 | 2 | 0.0 | 0 | 1 | 0 |
| Curtis Conway | WR | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Roman Fortin | OT | 2 | 2 | 0.0 | 0 | 0 | 0 |
| David Binn | LS | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Reggie Davis | TE | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Jeff Graham | WR | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Freddie Jones | TE | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Antoine Simpson | DT | 2 | 2 | 0.0 | 0 | 0 | 0 |
| Darren Bennett | P | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Jermaine Fazande | RB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Richard Harvey | LB | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Raleigh Roundtree | G | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Mikhael Ricks | TE | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Trevor Gaylor | WR | 1 | 1 | 0.0 | 0 | 0 | 0 |
| Leonardo Carson | DT | 1 | 1 | 0.0 | 0 | 0 | 0 |