2013 Salary Cap
| Player | Base Salary | Signing Bonus | Other Bonus | Cap Figure |
|---|---|---|---|---|
| Vernon Davis | 6,072,000 | 2,036,667 | 631,250 | 8,739,917 |
| Justin Smith | 7,500,000 | - | 500,000 | 8,000,000 |
| Carlos Rogers | 5,500,000 | 1,475,000 | 369,351 | 7,344,351 |
| Frank Gore | 3,300,000 | - | 3,150,000 | 6,450,000 |
| Michael Crabtree | 4,500,000 | 1,359,000 | 500,000 | 6,359,000 |
| Ahmad Brooks | 2,700,000 | 1,500,000 | 850,000 | 5,050,000 |
| Jonathan Goodwin | 3,700,000 | 666,667 | 650,000 | 5,016,667 |
| Mario Manningham | 3,600,000 | 1,000,000 | 350,000 | 4,950,000 |
| Donte Whitner | 3,850,000 | 833,333 | 250,000 | 4,933,333 |
| Andy Lee | 1,800,000 | 500,000 | 1,750,000 | 1,750,000 |
| Aldon Smith | 1,682,636 | 2,240,273 | - | 3,922,909 |
| Tarell Brown | 2,925,000 | 407,312 | 575,000 | 3,907,312 |
| David Akers | 3,000,000 | 566,66 | 750,000 | 3,616,667 |
| Patrick Willis | 2,402,000 | - | 1,203,125 | 3,605,125 |
| Anthony Davis | 1,300,000 | 166,667 | 2,100,000 | 3,566,667 |
| NaVorro Bowman | 630,000 | 1,675,562 | 800,000 | 3,105,562 |
| Parys Haralson | 2,570,000 | - | 300,000 | 2,870,000 |
| Joe Staley | 2,100,000 | - | 700,000 | 2,800,000 |
| Mike Iupati | 1,002,000 | 240,000 | 1,387,500 | 2,629,500 |
| Ray McDonald | 715,000 | 1,138,235 | 708,749 | 2,561,984 |
| Alex Boone | 950,000 | 340,000 | 650,000 | 1,940,000 |
| AJ Jenkins | 705,797 | 873,188 | - | 1,578,985 |
| CJ Spillman | 1,225,000 | 308,333 | 25,000 | 1,558,333 |
| Colin Kaepernick | 740,844 | 556,688 | 100,000 | 1,397,532 |
| Brian Jennings | 940,000 | 221,000 | - | 1,161,000 |
| LaMichael James | 490,859 | 213,250 | 50,000 | 754,109 |
| Chris Culliver | 555,000 | 149,719 | - | 704,719 |
| Kendall Hunter | 555,000 | 109,805 | - | 664,805 |
| Anthony Dixon | 630,000 | 30,150 | - | 660,150 |
| Kyle Williams | 630,000 | 19,850 | - | 649,850 |
| Daniel Kilgore | 555,000 | 40,075 | - | 595,075 |
| Joe Looney | 480,000 | 106,250 | - | 595,075 |
| Bruce Miller | 555,000 | 15,613 | - | 586,250 |
| Demarcus Dobbs | 555,000 | 4,166 | - | 559,166 |
| Lamar Divens | 555,000 | - | - | 555,000 |
| Chad Hall | 555,000 | - | - | 555,000 |
| Perrish Cox | 555,000 | - | - | 555,000 |
| Will Tukuafu | 555,000 | - | - | 555,000 |
| Scott Tolzien | 555,000 | - | - | 555,000 |
| Ian Williams | 555,000 | - | - | 555,000 |
| Darius Fleming | 480,000 | 41,200 | - | 521,200 |
| Trent Robinson | 480,000 | 27,625 | - | 507,625 |
| Garrett Celek | 480,000 | 2,000 | - | 482,000 |
| Jewel Hampton | 480,000 | 1,666 | - | 481,666 |
| Ricardo Lockette | 480,000 | - | - | 480,000 |
| Michael Wilhoite | 480,000 | - | - | 480,000 |
| Michael Thomas | 480,000 | - | - | 480,000 |
| Nathan Stupar | 405,000 | - | - | 405,00 |
| Kenny Wiggins | 405,000 | - | - | 405,00 |
| Al Netter | 405,000 | - | - | 405,00 |
| Wayne Tribue | 405,000 | - | - | 405,00 |
| Tony Jerod-Eddie | 405,000 | - | - | - |
| Cam Johnson | 405,000 | - | - | - |
| Joe Hastings | - | - | - | - |
