| Team Transactions |
| DATE | TRANSACTION |
| November 4, 2009 | Signed CB Keith Smith to a one-year contract. Released WR Micheal Spurlock. Released TE Carson Butler from the practice squad. |
| October 29, 2009 | Signed CB Tarell Brown to a three-year contract extension and OT Chris Patrick. Signed TE Carson Butler to the practice squad. |
| October 28, 2009 | Placed OT Tony Pashos on injured reserve. |
| October 22, 2009 | Signed RB Keon Lattimore to the practice squad. |
| October 20, 2009 | Placed LB Jeff Ulbrich on injured reserve. Signed LB Matt Wilhelm. |
| October 14, 2009 | Signed OL Khalif Mitchell to the practice squad. |
| October 13, 2009 | Signed OL Khalif Mitchell to the practice squad. |
| October 7, 2009 | Signed WR Michael Crabtree to a six-year contract. Signed OLB Martail Burnett to the practice squad. |
| September 7, 2009 | LB Diyral Briggs cut; OT Tony Pashos signed/unrestricted free agent; OT Alex Boone added to practice squad; WR Dobson Collins added to practice squad; TE J.J. Finley added to practice squad; FB Brit Miller added to practice squad; DT Khalif Mitchell added to practice squad; RB Kory Sheets added to practice squad; WR Dominique Zeigler added to practice squad |
| September 5, 2009 | OT Jacob Bender cut; OT Alex Boone cut; WR Dobson Collins cut; DE Pannel Egboh cut; TE J.J. Finley cut; OT Kyle Howard cut; CB Terrail Lambert cut; FB Brit Miller cut; DT Khalif Mitchell cut; LB Jay Moore cut; TE Bear Pascoe cut; WR Maurice Price cut; FB Bill Rentmeester cut; LB Justin Roland cut; RB Kory Sheets cut; C Matt Spanos cut; OT Joe Toledo cut; LB Mark Washington cut; WR Dominique Zeigler cut; OT Tony Pashos cut; CB Eric Green cut |
| September 2, 2009 | QB Damon Huard cut |
| August 31, 2009 | WR Mark Bradford cut; WR Chris Francies cut; PK Alexandre Romero cut; CB Carlos Thomas cut; CB Jahi Word-Daniels cut |
| August 24, 2009 | Activated defensive end Ray McDonald from the Active-Physically Unable to Perform List. |
| August 5, 2009 | Activated defensive lineman Ricky Jean-Francois from the Non-Football Illness list. |
| July 30, 2009 | Signed defensive lineman Babatunde Oshinowo. |
| July 28, 2009 | Signed running back Glen Coffee to a four-year contract. |
| July 25, 2009 | Signed quarterback Nate Davis to a four-year contract; waived safety Lewis Baker. |
| July 8, 2009 | Claimed fullback Brit Miller off waivers from the Carolina Panthers. |
| June 6, 2009 | Signed long snapper Brian Jennings to a five-year contract extension through 2014. |
| June 5, 2009 | Signed tackle Joe Staley to a six-year contract extension through 2017. |
| May 30, 2009 | Signed tight end Bear Pascoe to a four-year contract. |