| Team | W | L |
| 49ers | 13 | 3 |
| Cardinals | 8 | 8 |
| Seahawks | 7 | 9 |
| Rams | 2 | 14 |
| Reg | |||
| 9/9 | @Packers | 1:15pm | |
| 9/16 | Lions | 5:20pm | |
| 9/23 | @Vikings | 10:00am | |
| 9/30 | @Jets | 10:00am | |
| 10/7 | Bills | 1:15pm | |
| 10/14 | Giants | 1:15pm | |
| 10/18 | Seahawks | 5:20pm | |
| 10/29 | @Cardinals | 5:30pm | |
| 11/11 | Rams | 1:15pm | |
| 11/19 | Bears | 5:30pm | |
| 11/25 | @Saints | 1:15pm | |
| 12/2 | @Rams | 10:00am | |
| 12/9 | Dolphins | 1:05pm | |
| 12/16 | @Patriots | 5:20pm | |
| 12/23 | @Seahawks | 1:15pm | |
| 12/30 | Cardinals | 1:15pm | |
| Name | Pos. | Signed | 2012 Salary | Signing | Roster | Workout | Option | Incentive | Base | Other |
| Masifilo, Matt | DE | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Gonzales, David | OT | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Slowey, Jason | C | 2015 | $413,128 | $23,128 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Robinson, Trenton | FS | 2015 | $417,625 | $27,625 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Tavecchio, Giorgio | PK | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Purvis, Deante' | CB | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Hampton, Jewell | RB | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Johnson, Cam | OLB | 2015 | $401,750 | $11,750 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Holland, Joe | OLB | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Palmer, Nathan | WR | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Owusu, Chris | WR | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Netter, Al | OG | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| James, LaMichael | RB | 2015 | $603,250 | $213,250 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Jenkins, A.J. | WR | 2015 | $0 | $0 | $0 | $0 | $0 | $0 | $0 | $0 |
| Jerod-Eddie, Tony | DE | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Looney, Joe | OG | 2015 | $496,250 | $106,250 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Mosley, Anthony | CB | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Hannula, Ben | CB | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Brown, Kourtnei | OLB | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Bell, Cameron | FB | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Thomas, Michael | S | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Bakhtiari, Eric | OLB | 2013 | $465,000 | $0 | $0 | $0 | $0 | $0 | $465,000 | $0 |
| Tyms, Brian | WR | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Fleming, Darius | OLB | 2015 | $431,000 | $41,000 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Butrym, Patrick | DE | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Celek, Garrett | TE | 2014 | $390,000 | $0 | $0 | $0 | $0 | $0 | $390,000 | $0 |
| Wiggins, Kenny | OT | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Williams, Ian | NT | 2013 | $470,580 | $0 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Nelson, Kyle | LS | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Williams, Kyle | WR | 2013 | $565,430 | $19,850 | $0 | $0 | $0 | $0 | $540,000 | $5580 |
| Nelms, Cory | CB | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Willis, Patrick | ILB | 2016 | $17,642,287 | $14,173,332 | $1,059,375 | $500,000 | $0 | $0 | $1,904,000 | $5580 |
| Miller, Bruce | FB | 2014 | $486,193 | $15,613 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| McDonald, Ray | DE | 2015 | $4,155,580 | $1,000,000 | $0 | $100,000 | $0 | $0 | $3,050,000 | $5580 |
| Manningham, Mario | WR | 2013 | $2,555,580 | $1,000,000 | $250,000 | $100,000 | $0 | $0 | $1,200,000 | $5580 |
| Swain, Brett | WR | 2012 | $620,580 | $0 | $0 | $0 | $0 | $0 | $615,000 | $5580 |
| Whitner, Donte | SS | 2013 | $4,388,913 | $833,333 | $0 | $250,000 | $0 | $0 | $3,300,000 | $5580 |
| Person, Mike | OG | 2014 | $482,055 | $11,475 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Staley, Joe | LT | 2017 | $2,700,580 | $0 | $695,000 | $200,000 | $0 | $0 | $1,800,000 | $5580 |
| Reuland, Konrad | TE | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Sopoaga, Isaac | NT | 2012 | $4,960,580 | $955,000 | $200,000 | $0 | $0 | $0 | $3,800,000 | $5580 |
| Smith, Justin | DE | 2013 | $6,380,580 | $0 | $0 | $500,000 | $0 | $0 | $5,875,000 | $5580 |
| Smith, Alex | QB | 2014 | $9,255,580 | $0 | $3,000,000 | $0 | $0 | $1,250,000 | $5,000,000 | $5580 |
| Smith, Aldon | OLB | 2014 | $3,274,671 | $2,240,273 | $0 | $0 | $0 | $0 | $1,028,818 | $5580 |
| Tolzien, Scott | QB | 2013 | $470,580 | $0 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Rogers, Carlos | CB | 2015 | $5,505,580 | $1,250,000 | $250,000 | $100,000 | $0 | $0 | $3,900,000 | $5580 |
| Tukuafu, Will | DE | 2013 | $470,580 | $0 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Wilhoite, Michael | OLB | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Walker, Delanie | TE | 2012 | $2,010,580 | $360,000 | $500,000 | $100,000 | $0 | $0 | $1,045,000 | $5580 |
| Spillman, C.J. | SS | 2014 | $1,085,580 | $330,000 | $0 | $0 | $0 | $0 | $750,000 | $5580 |
| Pontbriand, Ryan | LS | 2012 | $831,580 | $0 | $0 | $0 | $0 | $0 | $826,000 | $5580 |
| Moss, Randy | WR | 2012 | $2,505,580 | $0 | $750,000 | $0 | $0 | $0 | $1,750,000 | $5580 |
| LeGree, Mark | FS | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Ginn Jr., Ted | WR | 2012 | $1,380,580 | $0 | $175,000 | $0 | $0 | $0 | $1,200,000 | $5580 |
| Akers, David | PK | 2013 | $3,622,247 | $566,667 | $0 | $0 | $0 | $50,000 | $3,000,000 | $5580 |
| Dobbs, Demarcus | DE | 2013 | $470,580 | $0 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Dixon, Anthony | RB | 2013 | $575,730 | $30,150 | $0 | $0 | $0 | $0 | $540,000 | $5580 |
| Davis, Vernon | TE | 2015 | $8,023,246 | $1,666,666 | $400,000 | $200,000 | $0 | $0 | $5,751,000 | $5580 |
| Davis, Anthony | RT | 2014 | $3,197,246 | $166,666 | $0 | $400,000 | $1,700,000 | $0 | $925,000 | $5580 |
| Culliver, Chris | CB | 2014 | $620,299 | $149,719 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Crabtree, Michael | WR | 2014 | $5,364,580 | $1,359,000 | $500,000 | $0 | $0 | $0 | $3,500,000 | $5580 |
| Cox, Perrish | CB | 2013 | $470,580 | $0 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Chisolm, Garrett | OG | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Cartwright, Rock | RB | 2012 | $955,580 | $25,000 | $0 | $0 | $0 | $0 | $925,000 | $5580 |
| Byham, Nate | TE | 2013 | $522,130 | $26,550 | $0 | $0 | $0 | $0 | $490,000 | $5580 |
| Brown, Tarell | CB | 2013 | $1,736,330 | $880,750 | $0 | $0 | $0 | $0 | $850,000 | $5580 |
| Brooks, Ahmad | OLB | 2017 | $2,855,580 | $1,500,000 | $500,000 | $100,000 | $0 | $0 | $750,000 | $5580 |
| Brock, Tramaine | CB | 2012 | $545,580 | $0 | $0 | $0 | $0 | $0 | $540,000 | $5580 |
| Bowman, NaVorro | ILB | 2013 | $721,142 | $175,562 | $0 | $0 | $0 | $0 | $540,000 | $5580 |
| Boone, Alex | RT | 2015 | $935,580 | $340,000 | $0 | $50,000 | $0 | $0 | $540,000 | $5580 |
| Goldson, Dashon | FS | 2012 | $6,212,000 | $0 | $0 | $0 | $0 | $0 | $6,212,000 | $5580 |
| Gooden, Tavares | ILB | 2012 | $705,580 | $0 | $0 | $0 | $0 | $0 | $700,000 | $5580 |
| Lee, Andy | P | 2012 | $1,382,248 | $276,668 | $0 | $0 | $0 | $0 | $1,100,000 | $5580 |
| Kilgore, Daniel | OG | 2014 | $510,655 | $40,075 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Kaepernick, Colin | QB | 2014 | $1,170,193 | $556,691 | $0 | $0 | $0 | $0 | $607,922 | $5580 |
| Jones, Colin | FS | 2014 | $470,580 | $0 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Johnson, Josh | QB | 2013 | $880,580 | $175,000 | $0 | $0 | $0 | $0 | $750,000 | $5580 |
| Hastings, Joe | WR | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Jennings, Brian | LS | 2014 | $1,151,580 | $221,000 | $0 | $0 | $0 | $0 | $925,000 | $5580 |
| Jean Francois, Ricky | NT | 2012 | $631,330 | $10,750 | $0 | $0 | $0 | $0 | $615,000 | $5580 |
| Jacobs, Brandon | RB | 2012 | $1,580,580 | $150,000 | $475,000 | $0 | $0 | $0 | $950,000 | $5580 |
| Iupati, Mike | LG | 2014 | $2,036,580 | $240,000 | $0 | $0 | $1,087,500 | $0 | $703,500 | $5580 |
| Hunter, Kendall | RB | 2014 | $580,385 | $109,805 | $0 | $0 | $0 | $0 | $465,000 | $5580 |
| Holcomb, Curtis | CB | 2014 | $401,475 | $11,475 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Haralson, Parys | OLB | 2013 | $2,755,580 | $0 | $200,000 | $100,000 | $0 | $0 | $2,450,000 | $5580 |
| Hall, Derek | OT | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
| Grant, Larry | ILB | 2012 | $1,265,580 | $0 | $0 | $0 | $0 | $0 | $1,260,000 | $5580 |
| Gore, Frank | RB | 2014 | $6,005,580 | $0 | $3,250,000 | $750,000 | $0 | $0 | $2,000,000 | $5580 |
| Goodwin, Jonathan | C | 2013 | $3,722,247 | $666,667 | $0 | $0 | $0 | $650,000 | $2,400,000 | $5580 |
| Beeler, Chase | C | 2013 | $395,580 | $0 | $0 | $0 | $0 | $0 | $390,000 | $5580 |
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