Transactions
| Date | Player | Pos | Transactions |
| 7/6 | Jamar Taylor | CB | signed/unrest FA One-year contract (through 2020) |
| 7/6 | Teez Tabor | CB | cut |
| 6/26 | Javon Kinlaw | DT | signed/draft choice Four-year contract (fifth-year option) |
| 6/26 | Brandon Aiyuk | WR | signed/draft choice Four-year contract (fifth-year option) |
| 6/24 | Jauan Jennings | WR | signed/draft choice Four-year contract (through 2023) |
| 6/19 | Colton McKivitz | T | signed/draft choice Four-year contract (through 2023) |
| 5/1 | Nick Mullens | QB | re-signed/excl. FA One-year contract (through 2020) |
| 5/1 | Solomon Thomas | DE | team declines option Fifth-year option on rookie contract |
| 5/1 | Salvon Ahmed | RB | signed |
| 4/28 | DeMarkus Acy | CB | signed |
| 4/28 | Darrion Daniels | DT | signed |
| 4/28 | Chris Finke | WR | signed |
| 4/28 | Jonas Griffith | LB | signed |
| 4/28 | Chase Harrell | TE | signed |
| 4/28 | JaMycal Hasty | RB | signed |
| 4/28 | Broc Rutter | QB | signed |
| 4/28 | Jared Mayden | S | signed |
| 4/28 | Josh Hokit | RB | signed |
| 4/27 | Jacob Thieneman | S | cut |
| 4/25 | Trent Williams | T | traded for 2020 and 2021 draft picks |
| 4/25 | Joe Staley | T | retired |
| 4/20 | Jeff Wilson Jr. | RB | re-signed/excl. FA One-year contract (through 2020) |
| 4/16 | Matt Breida | RB | re-signed/rest FA One-year contract (through 2020) |
| 4/13 | Dontae Johnson | CB | re-signed/unrest FA One-year contract (through 2020) |
| 4/13 | Jason Verrett | CB | re-signed/unrest FA One-year contract (through 2020) |
| 4/6 | Kendrick Bourne | WR | re-signed/rest FA One-year contract (through 2020) |
| 3/24 | Ross Dwelley | TE | re-signed/excl. FA One-year contract (through 2020) |
| 3/24 | Kerry Hyder | DE | signed/unrest FA One-year contract (through 2020) |
| 3/24 | Travis Benjamin | WR | signed/unrest FA One-year contract (through 2020) |
| 3/23 | Joe Walker | LB | signed/unrest FA One-year contract (through 2020) |
| 3/20 | Daniel Brunskill | T | re-signed/excl. FA One-year contract (through 2020) |
| 3/19 | Tom Compton | G | signed/unrest FA One-year contract (through 2020) |
| 3/19 | Mike Person | C | cut |
| 3/18 | Kendrick Bourne | WR | Restricted Free Agent |
| 3/18 | Matt Breida | RB | Restricted Free Agent |
| 3/18 | Garrett Celek | TE | Declared Free Agent |
| 3/18 | Sheldon Day | DT | Declared Free Agent |
| 3/18 | Dontae Johnson | CB | Declared Free Agent |
| 3/18 | Jordan Matthews | WR | Declared Free Agent |
| 3/18 | Earl Mitchell | DT | Declared Free Agent |
| 3/18 | Damontre Moore | DE | Declared Free Agent |
| 3/18 | Emmanuel Sanders | WR | Declared Free Agent |
| 3/18 | Levine Toilolo | TE | Declared Free Agent |
| 3/18 | Jason Verrett | CB | Declared Free Agent |
| 3/18 | Jimmie Ward | S | Declared Free Agent |
| 3/18 | Anthony Zettel | DE | Declared Free Agent |
| 3/18 | Andrew Lauderdale | T | Declared Free Agent |
| 3/18 | Elijah Lee | LB | Declared Free Agent |
| 3/18 | Ben Garland | G | Declared Free Agent |
| 3/18 | Ben Garland | G | re-signed/unrest FA One-year contract (through 2020) |
| 3/18 | Jimmie Ward | S | re-signed/unrest FA Three-year contract (through 2022) |
| 3/18 | Ronald Blair III | DT | Declared Free Agent |
| 3/18 | Ronald Blair III | DT | re-signed/unrest FA One-year contract (through 2020) |
| 3/16 | Arik Armstead | DT | re-signed Five-year extension (through 2024) |
| 3/16 | Shon Coleman | T | re-signed One-year extension (through 2020) |
| 3/5 | Emmanuel Moseley | CB | re-signed/excl. FA One-year contract (through 2020) |
Last updated Jul. 12, 1:20 A.M. ET
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