| Last updated: Thu, May 23, 2013, 02:03 EDT |
| Date | Player | Pos. | Transaction |
| 5/22 | Quinton Patton | WR | signed/draft choice, Four-year contract (through 2016) |
| 5/21 | Kyle Nelson | TE | acquired from waivers |
| 5/21 | Anthony Santella | P | cut |
| 5/14 | Jason Schepler | RB | signed |
| 5/10 | Quinton Dial | DT | signed/draft choice, Four-year contract (through 2016) |
| 5/10 | B.J. Daniels | QB | signed/draft choice, Four-year contract (through 2016) |
| 5/10 | Carter Bykowski | T | signed/draft choice, Four-year contract (through 2016) |
| 5/10 | Nick Moody | LB | signed/draft choice, Four-year contract (through 2016) |
| 5/10 | Marcus Cooper | CB | signed/draft choice, Four-year contract (through 2016) |
| 5/7 | Alex Debniak | RB | signed |
| 5/7 | Luke Marquardt | T | signed |
| 5/7 | Mike Purcell | NT | signed |
| 5/7 | D.J. Harper | RB | signed |
| 5/7 | Lawrence Okoye | DE | signed |
| 5/7 | Patrick Omameh | G | signed |
| 5/7 | Darryl Morris | CB | signed |
| 5/7 | Kevin McDermott | TE | signed |
| 5/7 | MarQueis Gray | RB | signed |
| 5/7 | Sherman Carter | C | signed |
| 5/7 | Anthony Santella | P | signed, One-year contract (through 2013) |
| 5/7 | Chuck Jacobs | WR | signed |
| 5/6 | Adam Snyder | G | signed, Two-year contract (through 2014) |
| 5/3 | Lowell Rose | CB | signed |
| 5/2 | Sherman Carter | C | signed |
| 5/2 | Darryl Morris | CB | signed |
| 5/2 | Patrick Omameh | G | signed |
| 5/2 | Mike Purcell | DT | signed |
| 5/2 | Kevin McDermott | TE | signed |
| 5/2 | MarQueis Gray | RB | signed |
| 5/2 | Lowell Rose | CB | signed |
| 4/18 | Cameron Morrah | TE | signed/unrestricted free agent |
| 4/15 | Tramaine Brock | CB | re-signed/restricted free agent, One-year contract (through 2013) |
| 4/5 | Anthony Davis | T | re-signed, Five-year extension (through 2019) |
| 4/3 | Nnamdi Asomugha | CB | signed/unrestricted free agent, One-year contract (through 2013) |
| 4/1 | Colt McCoy | QB | traded, for 5th & 7th-round picks in 2013 draft |
| 3/21 | Darcel McBath | S | re-signed/unrestricted free agent, One-year contract (through 2013) |
| 3/19 | Phil Dawson | K | signed/unrestricted free agent, One-year contract (through 2013) |
| 3/19 | Marlon Moore | WR | signed/unrestricted free agent, One-year contract (through 2013) |
| 3/16 | Craig Dahl | S | signed/unrestricted free agent, Three-year contract (through 2015) |
| 3/14 | Dan Skuta | LB | signed/unrestricted free agent, Two-year contract (through 2014) |
| 3/13 | Glenn Dorsey | DE | signed/unrestricted free agent, Two-year contract (through 2014) |
| 3/12 | Dashon Goldson | S | declared free agent |
| 3/12 | Delanie Walker | TE | declared free agent |
| 3/12 | Isaac Sopoaga | NT | declared free agent |
| 3/12 | Randy Moss | WR | declared free agent |
| 3/12 | Ricky Jean Francois | DT | declared free agent |
| 3/12 | Clark Haggans | LB | declared free agent |
| 3/12 | Larry Grant | LB | declared free agent |
| 3/12 | Darcel McBath | S | declared free agent |
| 3/12 | Tavares Gooden | LB | declared free agent |
| 3/12 | Ted Ginn Jr. | WR | declared free agent |
| 3/12 | Anquan Boldin | WR | traded, for 6th-round pick in 2013 draft |
| 3/12 | Tramaine Brock | CB | Restricted Free Agent |
| 3/12 | Leonard Davis | G | declared free agent |
| 3/11 | Ian Williams | NT | re-signed, Two-year extension (through 2015) |
| 3/7 | Joe Hastings | WR | signed |
| 3/6 | David Akers | K | cut |
| 2/28 | Joe Hastings | WR | signed |
| 2/11 | Michael Thomas | S | signed |
| 2/7 | Ricardo Lockette | WR | signed |
| 2/6 | Al Netter | G | signed |
| 2/6 | Kenny Wiggins | T | signed |
| 2/6 | Lamar Divens | DT | signed |
| 2/6 | Nate Stupar | LB | signed |
| 2/4 | Mario Manningham | WR | Taken off IR, torn left ACL, PCL |
| 2/4 | Demarcus Dobbs | TE | Taken off IR, knee |
| 2/4 | Kyle Williams | WR | Taken off IR, torn left ACL |
| 2/4 | Kendall Hunter | RB | Taken off IR, Achilles |
| 2/4 | Parys Haralson | LB | Taken off IR, undisclosed |
| 1/19 | Chad Hall | WR | Activated from the Practice Squad |
| 1/18 | Billy Cundiff | K | cut |
| 1/8 | Nate Stupar | LB | practice squad addition |
| 1/1 | Billy Cundiff | K | signed |
| 1/1 | Eric Bakhtiari | LB | cut |
| 12/31 | Brandon Jacobs | RB | cut |
| 12/31 | Brandon Jacobs | RB | suspension lifted |
| 12/28 | Mario Manningham | WR | Placed on IR, torn left ACL, PCL |
| 12/28 | Tony Jerod-Eddie | DT | Activated from the Practice Squad, Three-year contract |
| 12/26 | Lamar Divens | DT | practice squad addition |
| 12/26 | Curtis Taylor | S | practice squad addition |
| 12/24 | Alex Hoffman-Ellis | LB | practice squad deletion |
| 12/22 | Cam Johnson | LB | Activated from the Practice Squad |
| 12/17 | Chad Hall | WR | practice squad addition |
| 12/14 | Chad Hall | WR | practice squad deletion |
| 12/12 | Eric Bakhtiari | LB | signed, Two-year contract (through 2013) |
| 12/11 | Demarcus Dobbs | TE | Placed on IR, knee |
| 12/10 | Brandon Jacobs | RB | suspended, 3 games (conduct detrimental to team) |
| 12/4 | Alex Hoffman-Ellis | LB | practice squad addition |
| 12/4 | Eddie Whitley | S | practice squad deletion |
| 11/30 | Michael Wilhoite | LB | Activated from the Practice Squad |
| 11/30 | Eddie Whitley | S | practice squad addition |
| 11/27 | Chad Hall | WR | practice squad addition |
| 11/27 | Jewel Hampton | RB | Activated from the physically unable to perform list |
| 11/27 | NaVorro Bowman | LB | re-signed, Five-year extension (through 2018) |
| 11/27 | Eddie Whitley | S | practice squad deletion |
| 11/27 | Kyle Williams | WR | Placed on IR, torn left ACL |
| 11/27 | Kendall Hunter | RB | Placed on IR, Achilles |
| More Transactions |
