Transactions
| Date | Player | Pos | Transactions |
| 2/4 | Kentavius Street | DE | reinstated |
| 2/4 | Jerick McKinnon | RB | off IR torn right ACL |
| 2/4 | Brock Coyle | LB | off IR concussion |
| 2/4 | Jimmy Garoppolo | QB | off IR torn left ACL |
| 2/4 | Adrian Colbert | CB | off IR ankle |
| 2/4 | Emmanuel Moseley | CB | off IR dislocated shoulder |
| 2/4 | Raheem Mostert | RB | off IR fractured forearm |
| 2/4 | Jimmie Ward | S | off IR broken forearm |
| 2/4 | Dekoda Watson | LB | off IR torn calf |
| 2/4 | Pierre Garcon | WR | off IR knee |
| 2/4 | Ahkello Witherspoon | CB | off IR knee |
| 2/4 | Jaquiski Tartt | S | off IR shoulder |
| 2/4 | Matt Breida | RB | off IR ankle |
| 2/4 | Dante Pettis | WR | off IR knee |
| 1/5 | JP Flynn | T | cut |
| 1/5 | JP Flynn | T | off IR undisclosed |
| 1/4 | Kapron Lewis-Moore | DT | signed |
| 12/31 | Kyle Nelson | TE | suspension lifted |
| 12/31 | Christian DiLauro | T | signed |
| 12/31 | Marcus Lucas | TE | signed |
| 12/31 | Tarvarus McFadden | CB | signed |
| 12/31 | Jordan Smallwood | WR | signed |
| 12/31 | Najee Toran | G | signed |
| 12/31 | Terrell Williams Jr. | S | signed |
| 12/29 | Ryan Delaire | DE | active/prac. squad |
| 12/29 | Max McCaffrey | WR | active/prac. squad |
| 12/29 | Matt Breida | RB | on IR ankle |
| 12/29 | Dante Pettis | WR | on IR knee |
| 12/26 | Steven Dunbar Jr. | WR | active/prac. squad |
| 12/21 | Jaquiski Tartt | S | on IR shoulder |
| 12/19 | Jordan Smallwood | WR | pract. squad add |
| 12/18 | Tyvis Powell | S | signed |
| 12/18 | Ahkello Witherspoon | CB | on IR knee |
| 12/11 | Tyree Robinson | S | active/prac. squad |
| 12/11 | Marcus Lucas | TE | pract. squad add |
| 12/11 | Pierre Garcon | WR | on IR knee |
| 12/5 | Colin Holba | C | signed |
| 12/5 | Pita Taumoepenu | LB | active/prac. squad |
| 12/5 | Terrell Williams Jr. | S | pract. squad add |
| 12/5 | Dekoda Watson | LB | on IR torn calf |
| 12/4 | Kyle Nelson | TE | suspended 10 games (by NFL) |
| 11/27 | Godwin Igwebuike | S | acquired from waiver |
| 11/27 | James Onwualu | LB | active/prac. squad |
| 11/27 | Tyrell Adams | LB | pract. squad add |
| 11/27 | Max McCaffrey | WR | pract. squad add |
| 11/27 | Jimmie Ward | S | on IR broken forearm |
| 11/25 | Reuben Foster | LB | cut |
| 11/24 | Jeff Wilson Jr. | RB | active/prac. squad |
| 11/24 | Tom Savage | QB | cut |
| 11/19 | James Onwualu | LB | pract. squad add |
| 11/12 | Matt Dayes | RB | active/prac. squad |
| 11/12 | Tyvis Powell | S | cut |
| 11/8 | Greg Mabin | CB | active/prac. squad |
| 11/8 | Tarvarus McFadden | CB | pract. squad add |
| 11/3 | Tom Savage | QB | signed |
| 11/3 | Emmanuel Moseley | CB | on IR dislocated shoulder |
| 11/3 | Raheem Mostert | RB | on IR fractured forearm |
| 11/1 | Emmanuel Moseley | CB | active/prac. squad |
| 11/1 | Tom Savage | QB | cut |
| 11/1 | Aaron Burbridge | WR | pract. squad del |
| 11/1 | Victor Bolden Jr. | WR | pract. squad add |
| 11/1 | Greg Mabin | CB | pract. squad add |
| 10/30 | Victor Bolden Jr. | WR | cut |
| 10/30 | Greg Mabin | CB | cut |
| 10/23 | Aaron Burbridge | WR | pract. squad add |
| 10/22 | Tom Savage | QB | signed |
| 10/22 | Adrian Colbert | CB | on IR ankle |
| 10/20 | Tyvis Powell | S | active/prac. squad |
| 10/20 | Tom Savage | QB | cut |
| 10/17 | Ryan Delaire | DE | pract. squad add |
| 10/17 | Cole Wick | TE | pract. squad add |
| 10/16 | Tom Savage | QB | signed One-year contract (through 2018) |
| 10/16 | Cole Wick | TE | cut |
| 10/16 | Zack Golditch | G | pract. squad del |
| 10/15 | Ross Dwelley | TE | active/prac. squad |
| 10/15 | Ryan Delaire | DE | cut |
| 10/9 | Dexter McCoil | S | pract. squad del |
| 10/9 | Frank Stephens | WR | pract. squad del |
| 10/9 | Matt Dayes | RB | pract. squad add |
| 10/9 | Najee Toran | G | pract. squad add |
| 10/9 | Tyvis Powell | S | pract. squad add |
| 10/6 | Ryan Delaire | DE | active/prac. squad |
| 10/6 | Tyvis Powell | S | cut |
| 10/6 | Najee Toran | G | cut |
| 10/1 | Victor Bolden Jr. | WR | suspension lifted |
| 9/26 | Nick Mullens | QB | active/prac. squad |
| 9/26 | Ryan Delaire | DE | pract. squad add |
| 9/26 | Christian DiLauro | T | pract. squad add |
| 9/26 | Dexter McCoil | S | pract. squad add |
| 9/26 | Jimmy Garoppolo | QB | on IR torn left ACL |
| 9/22 | Tyvis Powell | S | active/prac. squad |
| 9/22 | Terence Garvin | LB | cut |
| 9/19 | Matt Tobin | T | cut |
| 9/17 | Reuben Foster | LB | suspension lifted |
| 9/12 | Terence Garvin | LB | signed One-year contract (through 2018) |
| 9/12 | Najee Toran | G | active/prac. squad |
| 9/12 | Frank Stephens | WR | pract. squad add |
| 9/12 | Aaron Burbridge | WR | cut |
| 9/12 | Aaron Burbridge | WR | off IR undisclosed |
| 9/12 | Brock Coyle | LB | on IR concussion |
| 9/7 | Malcolm Johnson | RB | cut |
| 9/7 | Malcolm Johnson | RB | off IR undisclosed |
| 9/6 | Daeshon Hall | DE | pract. squad add |
| 9/6 | Niles Scott | pract. squad del | |
| 9/3 | Zack Golditch | G | pract. squad add |
| 9/3 | Antone Exum Jr. | S | signed |
| 9/3 | Matt Tobin | T | signed |
| 9/3 | Jerick McKinnon | RB | on IR torn right ACL |
| 9/2 | Steven Dunbar Jr. | WR | pract. squad add |
| 9/2 | Ross Dwelley | TE | pract. squad add |
| 9/2 | Emmanuel Moseley | CB | pract. squad add |
| 9/2 | Nick Mullens | QB | pract. squad add |
| 9/2 | Tyvis Powell | S | pract. squad add |
| 9/2 | Niles Scott | pract. squad add | |
| 9/2 | Pita Taumoepenu | LB | pract. squad add |
| 9/2 | Najee Toran | G | pract. squad add |
| 9/2 | Jeff Wilson Jr. | RB | pract. squad add |
| 9/2 | Aaron Burbridge | WR | on IR undisclosed |
| 9/2 | JP Flynn | T | on IR undisclosed |
| 9/2 | Malcolm Johnson | RB | on IR undisclosed |
| 9/1 | Jeremiah Attaochu | LB | cut |
| 9/1 | Jonathan Cooper | G | cut |
| 9/1 | Steven Dunbar Jr. | WR | cut |
| 9/1 | Ross Dwelley | TE | cut |
| 9/1 | Antone Exum Jr. | S | cut |
| 9/1 | Cole Hikutini | TE | cut |
| 9/1 | Andrew Lauderdale | T | cut |
| 9/1 | Dexter McCoil | S | cut |
| 9/1 | Tarvarus McFadden | CB | cut |
| 9/1 | Jeremy McNichols | RB | cut |
| 9/1 | Emmanuel Moseley | CB | cut |
| 9/1 | Nick Mullens | QB | cut |
| 9/1 | Tyvis Powell | S | cut |
| 9/1 | Niles Scott | cut | |
| 9/1 | Coleman Shelton | G | cut |
| 9/1 | Pita Taumoepenu | LB | cut |
| 9/1 | Korey Toomer | LB | cut |
| 9/1 | Najee Toran | G | cut |
| 9/1 | Jeff Wilson Jr. | RB | cut |
| 9/1 | Kentavius Street | DE | reserve/non football injury |
| 8/31 | Shon Coleman | T | traded for 2019 seventh-round draft pick |
| 8/31 | Ja'Quan Gardner | RB | cut |
| 8/31 | Chris Gonzalez | G | cut |
| 8/31 | Jack Heneghan | QB | cut |
| 8/31 | Chris Jones | DT | cut |
| 8/31 | Jeff Locke | P | cut |
| 8/31 | Pace Murphy | T | cut |
| 8/31 | Aldrick Robinson | WR | cut |
| 8/31 | Wes Saxton | TE | cut |
| 8/31 | Will Sutton | DT | cut |
| 8/31 | Darrell Williams Jr. | T | cut |
| 8/31 | Joe Williams | RB | cut |
| 8/30 | Elvis Dumervil | DE | retired |
| 8/29 | Max McCaffrey | WR | cut |
| 8/28 | Ja'Quan Gardner | RB | signed |
| 8/28 | Chanceller James | S | cut |
| 8/22 | Cedric Thornton | DT | retired |
| 8/22 | Chris Jones | DT | signed One-year contract (through 2018) |
| 8/21 | Terrell Williams Jr. | S | cut |
| 8/21 | Terrell Williams Jr. | S | off IR undisclosed |
| 8/17 | Dexter McCoil | S | signed |
| 8/17 | Terrell Williams Jr. | S | on IR undisclosed |
| 8/14 | Alfred Morris | RB | signed/unrest FA |
| 8/14 | Alan Knott | C | cut |
| 8/5 | Chris Gonzalez | G | signed One-year contract (through 2018) |
| 8/5 | Corey Griffin | S | cut |
| 7/31 | Wes Saxton | TE | signed One-year contract (through 2018) |
| 7/31 | C.J. Goodwin | CB | cut |
| 7/26 | JP Flynn | T | signed Two-year contract (through 2019) |
| 7/26 | Will Sutton | DT | signed One-year contract (through 2018) |
| 7/26 | Cedric Thornton | DT | signed/unrest FA One-year contract (through 2018) |
| 7/26 | Don Jones | S | cut |
| 7/26 | Jamar McGloster | T | cut |
| 7/26 | Blaine Woodson | DE | cut |
| 7/25 | Dante Pettis | WR | signed Four-year contract (through 2021) |
| 7/23 | Mike McGlinchey | T | signed/draft choice Four-year contract (fifth-year option) |
| 7/3 | Reuben Foster | LB | suspended 2 games (NFL Substance Abuse Policy) |
| 6/22 | Laken Tomlinson | G | re-signed Three-year extension (through 2021) |
| 6/13 | Fred Warner | LB | signed/draft choice Four-year contract (through 2021) |
| 6/6 | Antone Exum Jr. | S | re-signed/unrest FA One-year contract (through 2018) |
| 6/4 | Trovon Reed | CB | cut |
| 6/1 | Victor Bolden Jr. | WR | suspended 4 games (NFL Policy on PEDs) |
| 5/15 | C.J. Goodwin | CB | acquired from waiver |
| 5/15 | DeAndre Carter | WR | cut |
| 5/15 | Blaine Woodson | DE | signed |
| 5/14 | Marcell Harris | S | signed/draft choice Four-year contract (through 2021) |
| 5/11 | D.J. Reed Jr. | CB | signed/draft choice Four-year contract (through 2021) |
| 5/9 | Mike Person | C | signed/unrest FA One-year contract (through 2018) |
| 5/7 | Zane Beadles | G | cut |
| 5/7 | Kentavius Street | DE | signed/draft choice Four-year contract (through 2021) |
| 5/5 | Richie James Jr. | WR | signed/draft choice Four-year contract (through 2021) |
| 5/5 | Tarvarius Moore | S | signed/draft choice Four-year contract (through 2021) |
| 5/5 | Jullian Taylor | DT | signed/draft choice Four-year contract (through 2021) |
| 5/2 | Coleman Shelton | G | signed |
| 5/2 | Jeff Wilson Jr. | RB | signed |
| 5/2 | Laken Tomlinson | G | team declines option Fifth-year option on rookie contract |
| 5/1 | Corey Griffin | S | signed Three-year contract (through 2020) |
| 5/1 | Tarvarus McFadden | CB | signed Three-year contract (through 2020) |
| 5/1 | Emmanuel Moseley | CB | signed Three-year contract (through 2020) |
| 5/1 | Najee Toran | G | signed Three-year contract (through 2020) |
| 4/30 | Arik Armstead | DT | team exercises option Fifth-year option on rookie contract |
| 4/30 | Jimmie Gilbert | LB | cut |
| 4/30 | Bo Lokombo | LB | cut |
| 4/30 | Dexter McCoil | S | cut |
| 4/30 | Donavin Newsom | LB | cut |
| 4/30 | Channing Stribling | CB | cut |
| 4/30 | Steven Dunbar Jr. | WR | signed |
| 4/30 | Ross Dwelley | TE | signed |
| 4/30 | Jack Heneghan | QB | signed |
| 4/30 | Alan Knott | C | signed |
| 4/30 | Jamar McGloster | T | signed |
| 4/30 | Terrell Williams Jr. | S | signed |
| 4/30 | Niles Scott | signed | |
| 4/27 | Jaquiski Tartt | S | re-signed Two-year extension (through 2020) |
| 4/4 | Korey Toomer | LB | signed/unrest FA One-year contract (through 2018) |
| 3/20 | Jonathan Cooper | G | signed/unrest FA One-year contract (through 2018) |
| 3/15 | Jeremiah Attaochu | LB | signed/unrest FA One-year contract (through 2018) |
| 3/14 | Tim Barnes | C | Declared Free Agent |
| 3/14 | Tank Carradine | DE | Declared Free Agent |
| 3/14 | Brock Coyle | LB | Declared Free Agent |
| 3/14 | Leger Douzable | DE | Declared Free Agent |
| 3/14 | Elvis Dumervil | DE | Declared Free Agent |
| 3/14 | Antone Exum Jr. | S | Declared Free Agent |
| 3/14 | Brandon Fusco | G | Declared Free Agent |
| 3/14 | Leon Hall | CB | Declared Free Agent |
| 3/14 | Carlos Hyde | RB | Declared Free Agent |
| 3/14 | Asa Jackson | CB | Declared Free Agent |
| 3/14 | Dontae Johnson | CB | Declared Free Agent |
| 3/14 | Chris Jones | DT | Declared Free Agent |
| 3/14 | Aaron Lynch | LB | Declared Free Agent |
| 3/14 | Louis Murphy | WR | Declared Free Agent |
| 3/14 | Logan Paulsen | TE | Declared Free Agent |
| 3/14 | Eric Reid | S | Declared Free Agent |
| 3/14 | Brock Coyle | LB | re-signed/unrest FA Three-year contract (through 2020) |
| 3/14 | Jerick McKinnon | RB | signed/unrest FA Four-year contract (through 2021) |
| 3/14 | Weston Richburg | C | signed/unrest FA Five-year contract (through 2022) |
| 3/12 | Raheem Mostert | RB | re-signed/excl. FA One-year tender (through 2018) |
| 3/12 | Jeff Locke | P | signed One-year contract (through 2018) |
| 3/11 | Richard Sherman | CB | signed Three-year contract (through 2020) |
| 3/8 | Marquise Goodwin | WR | re-signed Three-year extension (through 2021) |
| 2/27 | Garry Gilliam | T | re-signed Two-year extension (through 2019) |
Last updated Feb. 6, 1:23 A.M. ET
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