| Category | Record | Record Holder |
| Total Points | 1,130 | Jerry Rice |
| Total Touchdowns | 187 | Jerry Rice |
| Field Goals Made | 190 | Ray Wershing |
| Longest Field Goal | 56 yds | Joe Nedney, Mike Cofer |
| Rushing Yards Gained | 7,344 yds | Joe Perry |
| Rushing Yards Season | 1,695 yds | Frank Gore |
| Rushing Yards Game | 212 yds | Frank Gore |
| 100 Yard Rushing Games | 20 | Joe Perry |
| 100 Yard Rusing Games Season | 9 | Frank Gore |
| Rushing Touchdowns | 50 | Roger Craig |
| Passing Yards | 35, 124 yds | Joe Montana |
| Passing Yards Season | 4,298 yds | Jeff Garcia |
| Passing Yards Game | 476 yds | Joe Montana |
| 300 Yard Passing Games | 35 | Joe Montana |
| 300 Yard Passing Game Season | 7 | Steve Young |
| Touchdown Passes | 244 | Joe Montana |
| Touchdown Passes Season | 36 | Steve Young |
| Touchdown Passes Game | 6 | Joe Montana |
| Receptions | 1,281 | Jerry Rice |
| Receptions Season | 122 | Jerry Rice |
| Receptions Game | 20 | Terrell Owens |
| Reception Yards | 19,247 yds | Jerry Rice |
| Reception Yards Season | 1,848 yds | Jerry Rice |
| Reception Yards Game | 289 yds | Jerry Rice |
| Receiving Touchdowns | 176 | Jerry Rice |
| Receiving Touchdowns Season | 22 | Jerry Rice |
| Receiving Touchdowns Game | 6 | Jerry Rice |
| Interceptions | 51 | Ronnie Lott |
| Sacks | 113 | Cedric Hardman |
| Sacks Season | 18 | Cedric Hardman |
| Punt Return Yardage | 1,531 yds | Dana McLemore |
| Kickoff Return Yardage | 4,873 yds | Abe Woodson |
| Punt Average Yards | 44.7 yds | Tommy Davis |