Transactions
| Date | Player | Pos | Transactions |
| 10/16 | Malik Henry | WR | pract. squad del |
| 10/15 | Deontay Burnett | WR | pract. squad add |
| 10/3 | Dontae Johnson | CB | signed One-year contract (through 2019) |
| 10/3 | Will Holden | T | pract. squad add |
| 10/3 | Jordan Matthews | WR | signed |
| 10/3 | Jalen Hurd | WR | on IR back |
| 10/3 | Jason Verrett | CB | on IR ankle |
| 10/2 | Marcell Harris | S | active/prac. squad |
| 10/2 | Antone Exum Jr. | S | cut |
| 10/1 | Jaryd Jones-Smith | T | pract. squad add |
| 10/1 | Will Holden | T | pract. squad del |
| 9/30 | Ryan Pope | T | pract. squad del |
| 9/30 | Teez Tabor | CB | pract. squad add |
| 9/24 | Garrison Sanborn | TE | signed/unrest FA One-year contract (through 2019) |
| 9/23 | Jon Condo | LB | retired |
| 9/20 | Sam Young | T | signed One-year contract (through 2019) |
| 9/20 | Trent Taylor | WR | on IR foot |
| 9/18 | Jon Condo | LB | signed/unrest FA One-year contract (through 2019) |
| 9/18 | Will Holden | T | pract. squad add |
| 9/17 | Colin Holba | C | cut |
| 9/14 | Jeff Wilson Jr. | RB | active/prac. squad |
| 9/14 | Kaden Smith | TE | cut |
| 9/6 | Adrian Colbert | CB | cut |
| 9/6 | Nick Williams | WR | cut |
| 9/6 | Nick Williams | WR | off IR undisclosed |
| 9/6 | Adrian Colbert | CB | off IR |
| 9/2 | Ryan Pope | T | pract. squad add |
| 9/1 | Kevin Givens | DT | pract. squad add |
| 9/1 | Marcell Harris | S | pract. squad add |
| 9/1 | Daniel Helm | TE | pract. squad add |
| 9/1 | Malik Henry | WR | pract. squad add |
| 9/1 | Elijah Lee | LB | pract. squad add |
| 9/1 | Ross Reynolds | G | pract. squad add |
| 9/1 | Jeremiah Valoaga | DE | pract. squad add |
| 9/1 | Jeff Wilson Jr. | RB | pract. squad add |
| 9/1 | Demetrius Flannigan-Fowles | LB | pract. squad add |
| 9/1 | Antone Exum Jr. | S | re-signed One-year contract (through 2019) |
| 9/1 | Adrian Colbert | CB | on IR |
| 9/1 | Andrew Lauderdale | T | on IR |
| 9/1 | Kentavius Street | DE | on IR |
| 8/31 | Jordan Matthews | WR | cut |
| 8/31 | Joshua Garnett | G | cut |
| 8/31 | Damontre Moore | DE | cut |
| 8/31 | Ross Reynolds | G | cut |
| 8/31 | Garrett Celek | TE | Placed on PUPL concussion |
| 8/31 | Antone Exum Jr. | S | cut |
| 8/31 | Demetrius Flannigan-Fowles | LB | cut |
| 8/31 | Jamell Garcia-Williams | DT | cut |
| 8/31 | Kevin Givens | DT | cut |
| 8/31 | Marcell Harris | S | cut |
| 8/31 | Daniel Helm | TE | cut |
| 8/31 | Malik Henry | WR | cut |
| 8/31 | Elijah Lee | LB | cut |
| 8/31 | David Mayo | LB | cut |
| 8/31 | LaRoy Reynolds | LB | cut |
| 8/31 | Tyree Robinson | S | cut |
| 8/31 | Wilton Speight | QB | cut |
| 8/31 | Chris Thompson | WR | cut |
| 8/31 | Jordan Thompson | DT | cut |
| 8/31 | Najee Toran | G | cut |
| 8/31 | Jeremiah Valoaga | DE | cut |
| 8/31 | Austin Walter | RB | cut |
| 8/31 | Jeff Wilson Jr. | RB | cut |
| 8/31 | Jerick McKinnon | RB | on IR knee |
| 8/31 | Nick Williams | WR | on IR undisclosed |
| 8/30 | Jay Bromley | DT | cut |
| 8/30 | Chris Campbell | CB | cut |
| 8/30 | Jordan Holland | CB | cut |
| 8/30 | Dontae Johnson | CB | cut |
| 8/30 | Wesley Johnson | C | cut |
| 8/30 | Tyree Mayfield | TE | cut |
| 8/30 | Quinten Rollins | CB | cut |
| 8/30 | Brandon Wilds | RB | cut |
| 8/30 | Sam Young | T | cut |
| 8/27 | Nick Williams | WR | signed One-year contract (through 2019) |
| 8/27 | Malcolm Smith | LB | cut |
| 8/27 | Chris Campbell | CB | signed One-year contract (through 2019) |
| 8/27 | Dillon Day | C | cut |
| 8/27 | Brandon Wilds | RB | signed One-year contract (through 2019) |
| 8/27 | Willie Beavers | G | cut |
| 8/26 | Jordan Holland | CB | signed Three-year contract (through 2021) |
| 8/26 | Greg Mabin | CB | cut |
| 8/26 | Greg Mabin | CB | off IR undisclosed |
| 8/26 | Tim Harris Jr. | CB | on IR undisclosed |
| 8/22 | Shawn Poindexter | WR | on IR torn ACL |
| 8/21 | Andrew Lauderdale | T | signed |
| 8/21 | Tyree Robinson | S | signed |
| 8/21 | Chris Thompson | WR | signed |
| 8/21 | Christian DiLauro | T | cut |
| 8/21 | Brandon Wilds | RB | cut |
| 8/17 | Greg Mabin | CB | on IR undisclosed |
| 8/16 | Quinten Rollins | CB | signed One-year contract (through 2019) |
| 8/12 | Kapron Lewis-Moore | DT | cut |
| 8/12 | Sam Young | T | signed/unrest FA One-year contract (through 2019) |
| 8/12 | Kapron Lewis-Moore | DT | off IR undisclosed |
| 8/12 | Shon Coleman | T | on IR fractured right fibula, dislocated ankle |
| 8/10 | Brandon Wilds | RB | signed One-year contract (through 2019) |
| 8/10 | Tyree Robinson | S | cut |
| 8/8 | Jeremiah Valoaga | DE | signed One-year contract (through 2019) |
| 8/8 | Chris Thompson | WR | cut |
| 8/3 | Jay Bromley | DT | signed/unrest FA One-year contract (through 2019) |
| 8/3 | Chris Thompson | WR | signed One-year contract (through 2019) |
| 8/3 | Max McCaffrey | WR | cut |
| 8/3 | Kapron Lewis-Moore | DT | on IR undisclosed |
| 8/2 | Niles Paul | TE | cut |
| 8/2 | Daniel Helm | TE | acquired from waiver |
| 8/2 | Erik Magnuson | T | cut |
| 8/2 | Erik Magnuson | T | off IR undisclosed |
| 7/27 | Jordan Thompson | DT | signed One-year contract (through 2019) |
| 7/26 | Nick Bosa | DE | signed/draft choice Four-year contract (fifth-year option) |
| 7/26 | Deebo Samuel | WR | signed/draft choice Four-year-contract (through 2022) |
| 7/26 | Dillon Day | C | signed One-year contract (through 2019) |
| 7/26 | Niles Paul | TE | signed One-year contract (through 2019) |
| 7/26 | Cedric Thornton | DT | cut |
| 7/26 | Erik Magnuson | T | on IR undisclosed |
| 7/25 | Alex Brown | CB | cut |
| 7/24 | Damontre Moore | DE | signed One-year contract (through 2019) |
| 7/23 | Jonathan Brown | K | cut |
| 7/22 | NaVorro Bowman | LB | signed/unrest FA One-day contract |
| 7/22 | NaVorro Bowman | LB | retired |
| 7/15 | Robbie Gould | K | re-signed Four-year contract (through 2022) |
| 6/5 | Joe Staley | T | re-signed Two-year extension (through 2021) |
| 5/28 | Pita Taumoepenu | LB | cut |
| 5/28 | Dontae Johnson | CB | signed One-year contract (through 2019) |
| 5/16 | Alex Brown | CB | signed Three-year contract (through 2021) |
| 5/16 | Damontre Moore | DE | cut |
| 5/15 | Levine Toilolo | TE | signed/unrest FA |
| 5/15 | Cameron Glenn | S | cut |
| 5/7 | Wesley Johnson | C | signed/unrest FA One-year contract (through 2019) |
| 5/7 | Marcus Lucas | TE | cut |
| 5/6 | LaRoy Reynolds | LB | signed/unrest FA One-year contract (through 2019) |
| 5/6 | Austin Walter | RB | signed Three-year contract (through 2021) |
| 5/6 | Ryan Delaire | DE | cut |
| 5/6 | Matt Dayes | RB | cut |
| 5/6 | Willie Beavers | G | acquired from waiver |
| 5/3 | Jalen Hurd | WR | signed/draft choice Four-year contract (through 2022) |
| 5/3 | Dre Greenlaw | LB | signed/draft choice Four-year contract (through 2022) |
| 5/3 | Kaden Smith | TE | signed/draft choice Four-year contract (through 2022) |
| 5/3 | Justin Skule | T | signed/draft choice Four-year contract (through 2022) |
| 5/3 | Tim Harris Jr. | CB | signed/draft choice Four-year contract (through 2022) |
| 5/3 | Azeez Al-Shaair | LB | signed |
| 5/3 | Demetrius Flannigan-Fowles | LB | signed |
| 5/3 | Jamell Garcia-Williams | DT | signed |
| 5/3 | Kevin Givens | DT | signed |
| 5/3 | Cameron Glenn | S | signed |
| 5/3 | Malik Henry | WR | signed |
| 5/3 | Tyree Mayfield | TE | signed |
| 5/3 | Shawn Poindexter | WR | signed |
| 5/3 | Ross Reynolds | G | signed |
| 5/3 | Wilton Speight | QB | signed |
| 5/2 | Joshua Garnett | G | team declines option Fifth-year option on rookie contract |
| 4/30 | Mitch Wishnowsky | P | signed/draft choice Four-year contract (through 2022) |
| 4/29 | Steven Dunbar Jr. | WR | cut |
| 4/29 | Godwin Igwebuike | S | cut |
| 4/29 | Tarvarus McFadden | CB | cut |
| 4/29 | James Onwualu | LB | cut |
| 4/29 | Jordan Smallwood | WR | cut |
| 4/29 | Justin Vogel | P | cut |
| 4/29 | Terrell Williams Jr. | S | cut |
| 4/24 | DeForest Buckner | DT | team exercises option Fifth-year option on rookie contract |
| 4/23 | Ben Garland | G | signed/unrest FA One-year contract (through 2019) |
| 4/15 | Greg Mabin | CB | re-signed/excl. FA One-year tender (through 2019) |
| 4/15 | Cedric Thornton | DT | reinstated |
| 4/12 | Daniel Brunskill | T | signed One-year contract (through 2019) |
| 4/5 | Damontre Moore | DE | signed One-year contract (through 2019) |
| 3/19 | Justin Vogel | P | signed One-year contract (through 2019) |
| 3/18 | Jimmie Ward | S | re-signed/unrest FA One-year contract (through 2019) |
| 3/15 | Antone Exum Jr. | S | re-signed/unrest FA One-year contract (through 2019) |
| 3/15 | Cassius Marsh | LB | cut |
| 3/15 | Mark Nzeocha | LB | re-signed/unrest FA Three-year contract (through 2021) |
| 3/15 | Raheem Mostert | RB | re-signed/rest FA Three-year contract (through 2021) |
| 3/14 | Elijah Lee | LB | re-signed/excl. FA One-year tender (through 2019) |
| 3/14 | Dee Ford | DE | signed Five-year contract (through 2023) |
| 3/14 | Tevin Coleman | RB | signed/unrest FA Two-year contract (through 2020) |
| 3/14 | Jason Verrett | CB | signed/unrest FA One-year contract (through 2019) |
| 3/14 | David Mayo | LB | signed/unrest FA Two-year contract (through 2020) |
| 3/14 | Brock Coyle | LB | cut |
| 3/14 | Jordan Matthews | WR | signed/unrest FA One-year contract (through 2019) |
| 3/13 | Raheem Mostert | RB | Restricted Free Agent |
| 3/13 | Antone Exum Jr. | S | Declared Free Agent |
| 3/13 | Pierre Garcon | WR | Declared Free Agent |
| 3/13 | Earl Mitchell | DT | Declared Free Agent |
| 3/13 | Alfred Morris | RB | Declared Free Agent |
| 3/13 | Mark Nzeocha | LB | Declared Free Agent |
| 3/13 | Bradley Pinion | P | Declared Free Agent |
| 3/13 | Jimmie Ward | S | Declared Free Agent |
| 3/13 | Tyvis Powell | S | Declared Free Agent |
| 3/13 | Kyle Nelson | TE | re-signed Four-year extension (through 2022) |
| 3/13 | Earl Mitchell | DT | team declines option |
| 3/13 | Dee Ford | DE | traded for 2020 second-round draft pick |
| 3/13 | Kwon Alexander | LB | signed/unrest FA Four-year contract (through 2022) |
| 3/8 | Jonathan Brown | K | signed Two-year contract (through 2020) |
| 3/7 | Kyle Juszczyk | RB | team exercises option One-year option (through 2019) |
| 3/7 | Cassius Marsh | LB | team exercises option One-year option (through 2019) |
| 3/7 | Dekoda Watson | LB | team exercises option One-year option (through 2019) |
| 3/7 | K'Waun Williams | CB | team exercises option One-year option (through 2019) |
| 3/7 | Pierre Garcon | WR | team declines option |
| 3/4 | Mike Person | C | re-signed Three-year extension (through 2021) |
| 2/26 | Robbie Gould | K | Designated franchise player non-exclusive franchise tag |
Last updated Oct. 17, 1:11 A.M. ET
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