| C. McCaffrey | RB | Faust, Banys, Becker-Parton | 2022–2025 | 50 | 998.0 | 20.0 |
| F. Gore | RB | Baumann, Ballard, Foote, Bronchtein | 2010–2014 | 74 | 794.6 | 10.7 |
| B. Aiyuk | WR | Banys | 2020–2023 | 50 | 543.1 | 10.9 |
| C. Hyde | RB | Waxman, Norberg | 2014–2017 | 61 | 470.6 | 7.7 |
| D. Samuel | WR | Banys, Valenzuela, Wright, Foote | 2019–2023 | 58 | 463.8 | 8.0 |
| V. Davis | TE | Baumann, Banys, Ballard, Freundlich | 2010–2014 | 75 | 458.4 | 6.1 |
| M. Crabtree | WR | Foote, Banys, Ballard, Bronchtein | 2010–2014 | 72 | 428.0 | 5.9 |
| B. Purdy | QB | Freundlich, P. Waxman | 2023–2025 | 30 | 370.3 | 12.3 |
| A. Boldin | WR | Banys, Valenzuela | 2013–2015 | 44 | 325.1 | 7.4 |
| J. Garoppolo | QB | Norberg, Banys, Sohl, Freundlich | 2017–2020 | 19 | 297.2 | 15.6 |
| D. Akers | K | Foote, Becker-Parton | 2011–2012 | 27 | 259.0 | 9.6 |
| Deebo Samuel | WR | Banys | 2021 | 16 | 256.6 | 16.0 |
| M. Breida | RB | Waxman, Sohl | 2018–2019 | 31 | 229.1 | 7.4 |
| P. Dawson | K | Waxman, Bronchtein, Foote, Ballard, Freundlich | 2013–2014 | 26 | 218.0 | 8.4 |
| R. Gould | K | Becker-Parton, Foote, Banys, Valenzuela, Baumann, Wright | 2018–2022 | 26 | 217.0 | 8.3 |
| Brock Purdy | QB | Wright, Baumann | 2024 | 15 | 208.7 | 13.9 |
| Brandon Aiyuk | WR | Freundlich, Ballard, Wright | 2021–2024 | 22 | 174.4 | 7.9 |
| R. Mostert | RB | Waxman, Wright, Baumann, Banys | 2018–2020 | 24 | 160.9 | 6.7 |
| E. Sanders | WR | Banys | 2019 | 15 | 151.4 | 10.1 |
| Elijah Mitchell | RB | Banys | 2021 | 15 | 130.6 | 8.7 |
| T. Coleman | RB | Wright, Becker-Parton | 2019–2020 | 15 | 129.9 | 8.7 |
| P. Garcon | WR | Freundlich, Ballard | 2017–2018 | 19 | 116.6 | 6.1 |
| J. Jennings | WR | Becker-Parton, Freundlich, Wright | 2025 | 13 | 116.3 | 8.9 |
| Jauan Jennings | WR | Faust, Bronchtein | 2024 | 11 | 108.7 | 9.9 |
| J. McKinnon | RB | Ballard | 2019–2020 | 30 | 108.6 | 3.6 |
| J. Moody | K | Banys, Faust | 2023 | 12 | 94.0 | 7.8 |
| A. Smith | QB | Banys, Foote, Norberg | 2010–2012 | 14 | 89.1 | 6.4 |
| Jake Moody | K | Waxman, Valenzuela, Ballard | 2024 | 9 | 79.0 | 8.8 |
| K. Hunter | RB | Banys, Freundlich | 2011–2013 | 14 | 72.3 | 5.2 |
| M. Goodwin | WR | Ballard, Banys | 2017–2018 | 11 | 67.5 | 6.1 |
| T. Smith | WR | Bronchtein, Wright | 2015–2016 | 11 | 64.5 | 5.9 |
| E. Pineiro | K | Waxman, Valenzuela | 2025 | 8 | 64.0 | 8.0 |
| M. Manningham | WR | Norberg, Banys | 2012–2013 | 23 | 63.6 | 2.8 |
| J. Dobbs | QB | Waxman, Banys, Foote, Faust | 2023 | 8 | 62.0 | 7.8 |
| J. Reed | K | Becker-Parton, Wright | 2010–2020 | 12 | 61.8 | 5.1 |
| R. Pearsall | WR | Valenzuela, P. Waxman | 2025 | 14 | 58.0 | 4.1 |
| J. Wilson | RB | Becker-Parton, Wright | 2018–2020 | 6 | 56.4 | 9.4 |
| Jimmy Garoppolo | QB | Banys, Faust | 2021 | 5 | 53.6 | 10.7 |
| Robbie Gould | K | Valenzuela, Freundlich | 2021 | 7 | 52.0 | 7.4 |
| Jeff Wilson | RB | Wright | 2021 | 14 | 48.0 | 3.4 |
| Isaac Guerendo | RB | Becker-Parton | 2024 | 4 | 47.2 | 11.8 |
| Trey Lance | QB | Wright, Becker-Parton | 2021 | 11 | 42.5 | 3.9 |
| Christian McCaffrey | RB | Wright | 2024 | 13 | 40.3 | 3.1 |
| V. McDonald | TE | Banys | 2016 | 9 | 38.8 | 4.3 |
| G. Celek | TE | Bronchtein | 2017 | 6 | 34.2 | 5.7 |
| B. Westbrook | RB | Banys | 2010 | 4 | 33.4 | 8.4 |
| A. Morris | RB | Baumann | 2018 | 7 | 31.1 | 4.4 |
| K. Bourne | WR | Faust | 2025 | 4 | 29.4 | 7.4 |
| E. Mitchell | RB | Valenzuela, Baumann, Wright | 2022–2023 | 19 | 28.3 | 1.5 |
| S. Draughn | RB | Freundlich, Baumann | 2015 | 4 | 26.5 | 6.6 |
| Trey Sermon | RB | Waxman | 2021 | 5 | 20.8 | 4.2 |
| B. Cundiff | K | Norberg | 2012 | 2 | 20.0 | 10.0 |
| J. Hasty | RB | Valenzuela | 2020 | 3 | 19.7 | 6.6 |
| D. Harris | WR | Wright | 2016 | 2 | 19.6 | 9.8 |
| R. Moss | WR | Banys | 2012 | 5 | 15.9 | 3.2 |
| Ricky Pearsall | WR | Baumann | 2024 | 2 | 15.3 | 7.7 |
| B. Robinson | RB | Becker-Parton, Valenzuela | 2025 | 5 | 14.5 | 2.9 |
| JaMycal Hasty | RB | Valenzuela | 2021 | 4 | 11.6 | 2.9 |
| Patrick Taylor | RB | Wright | 2024 | 3 | 11.5 | 3.8 |
| T. Lance | QB | Becker-Parton | 2022 | 2 | 11.5 | 5.7 |
| Demarcus Robinson | WR | Kassel | 2024 | 2 | 9.7 | 4.9 |
| A. Dixon | RB | Foote | 2010 | 4 | 6.5 | 1.6 |
| T. Taylor | QB | Banys, Wright | 2020 | 4 | 6.2 | 1.6 |
| J. Nedney | K | Banys | 2010 | 1 | 6.0 | 6.0 |
| J. Mason | RB | Valenzuela, Banys | 2022–2023 | 3 | 5.1 | 1.7 |
| B. Edwards | WR | Banys | 2011 | 2 | 4.8 | 2.4 |
| D. Pettis | WR | Baumann | 2019 | 1 | 1.2 | 1.2 |
| R. Bush | RB | Baumann | 2015 | 3 | 0.8 | 0.3 |
| Q. Patton | WR | Waxman | 2013 | 1 | 0.0 | 0.0 |
| I. Guerendo | RB | Freundlich | 2025 | 2 | 0.0 | 0.0 |