| Allen, Brandon |  SF | QB | UFA |  TEN |
| Anderson, Evan | SF | DT | ERFA | SF |
| Banks, Aaron | SF | OG | UFA |  GB |
| Barrett, Alex | SF | ED | ERFA | SF |
| Bartch, Ben | SF | OT | UFA | SF |
| Brown, Tre |  SEA | CB | UFA | SF |
| Campbell Sr., De'Vondre | SF | LB | UFA | |
| Collins, Maliek | SF | DT | CC |  CLE |
| Conley, Chris | SF | WR | UFA | |
| Davis, Khalil | SF | DT | UFA | |
| Dobbs, Joshua | SF | QB | UFA |  NE |
| Farrell, Luke |  JAX | TE | UFA | SF |
| Feliciano, Jon | SF | OG | UFA | |
| Flannigan-Fowles, Demetrius | SF | S | UFA |  NYG |
| Floyd, Leonard | SF | ED | CC |  ATL |
| Gifford, Luke | TEN | LB | UFA | SF |
| Gipson Sr., Tashaun | SF | S | UFA | |
| Givens, Kevin | SF | DT | UFA | SF |
| Graham, Jalen | SF | LB | ERFA | SF |
| Grant, Richie | ATL | S | UFA | SF |
| Greenlaw, Dre | SF | LB | UFA |  DEN |
| Hargrave, Javon | SF | DT | CC |  MIN |
| Heck, Charlie | SF | OT | UFA |  TB |
| Hufanga, Talanoa | SF | S | UFA | DEN |
| Jones, Mac | JAX | QB | UFA | SF |
| Juszczyk, Kyle | SF | FB | CC | SF |
| Mason, Jordan | SF | RB | RFA | SF |
| McCloud, Nick | SF | CB | UFA | |
| Mitchell, Elijah | SF | RB | UFA |  KC |
| Moore, Jaylon | SF | OT | UFA | KC |
| O'Donnell, Pat | SF | PT | UFA | |
| Okuayinonu, Sam | SF | ED | ERFA | SF |
| Pinnock, Jason | NYG | S | UFA | SF |
| Pleasants, Austen | SF | OT | ERFA | SF |
| Robinson, Curtis | SF | LB | RFA | SF |
| Robinson, Demarcus |  LAR | WR | UFA | SF |
| Samuel Sr., Deebo | SF | WR | Trade |  WAS |
| Saubert, Eric | SF | TE | UFA | |
| Taylor Jr., Patrick | SF | RB | UFA | SF |
| Tonges, Jake | SF | TE | ERFA | SF |
| Ward, Charvarius | SF | CB | UFA |  IND |
| Weeks, Jon |  HOU | LS | UFA | SF |
| Willis, Brayden | SF | TE | ERFA | SF |
| Ya-Sin, Rock | SF | CB | UFA | |
| Yiadom, Isaac | SF | CB | UFA |  NO |