| Team | W | L |
| 49ers | 13 | 3 |
| Cardinals | 8 | 8 |
| Seahawks | 7 | 9 |
| Rams | 2 | 14 |
| Pre | |||
| 12-Aug | @Saints | L | 3-24 |
| 20-Aug | Raiders | W | 17-3 |
| 27-Aug | Texans | L | 7-30 |
| 1-Sep | @Chargers | W | 20-17 |
| Reg | |||
| 11-Sep | Seahawks | W | 33-17 |
| 18-Sep | Cowboys | L | 24-27 |
| 25-Sep | @Bengals | W | 13-8 |
| 2-Oct | @Eagles | W | 24-23 |
| 9-Oct | Buccaneers | W | 48-3 |
| 16-Oct | @Lions | W | 25-19 |
| 30-Oct | Browns | W | 20-10 |
| 6-Nov | @Redskins | W | 19-11 |
| 13-Nov | Giants | W | 27-20 |
| 20-Nov | Cardinals | W | 23-7 |
| 24-Nov | @Ravens | L | 6-16 |
| 4-Dec | Rams | W | 26-0 |
| 11-Dec | @Cardinals | L | 19-21 |
| 19-Dec | Steelers | W | 20-3 |
| 24-Dec | @Seahawks | W | 19-17 |
| 1-Jan | @Rams | W | 34-27 |
| Name | Pos. | Signed | 2012 Salary | Signing | Roster | Workout | Base | Other |
| Willis, Patrick | ILB | 2016 | $17,642,287 | $14,173,332 | $1,059,375 | $500,000 | $1,904,000 | $5580 |
| Davis, Vernon | TE | 2015 | $8,023,246 | $1,666,666 | $400,000 | $200,000 | $5,751,000 | $5580 |
| Smith, Justin | DE | 2013 | $6,380,580 | $0 | $0 | $500,000 | $5,875,000 | $5580 |
| Gore, Frank | RB | 2014 | $6,005,580 | $0 | $3,250,000 | $750,000 | $2,000,000 | $5580 |
| Sopoaga, Isaac | NT | 2012 | $4,960,580 | $1,155,000 | $0 | $0 | $3,800,000 | $5580 |
| Whitner, Donte | SS | 2013 | $4,138,913 | $833,333 | $0 | $0 | $3,300,000 | $5580 |
| McDonald, Ray | DE | 2015 | $4,055,580 | $1,000,000 | $0 | $0 | $3,050,000 | $5580 |
| Crabtree, Michael | WR | 2014 | $4,005,580 | $0 | $0 | $500,000 | $3,500,000 | $5580 |
| Goodwin, Jonathan | C | 2013 | $3,722,247 | $666,667 | $650,000 | $0 | $2,400,000 | $5580 |
| Akers, David | PK | 2013 | $3,622,247 | $566,667 | $50,000 | $0 | $3,000,000 | $5580 |
| Spencer, Shawntae | CB | 2012 | $3,305,580 | $0 | $100,000 | $0 | $3,200,000 | $5580 |
| Smith, Aldon | OLB | 2014 | $3,274,671 | $2,240,273 | $0 | $0 | $1,028,818 | $5580 |
| Davis, Anthony | RT | 2014 | $2,797,246 | $166,666 | $1,700,000 | $0 | $925,000 | $5580 |
| Haralson, Parys | OLB | 2013 | $2,755,580 | $300,000 | $0 | $0 | $2,450,000 | $5580 |
| Staley, Joe | LT | 2017 | $2,505,580 | $695,000 | $0 | $0 | $1,800,000 | $5580 |
| Iupati, Mike | LG | 2014 | $2,036,580 | $240,000 | $1,087,500 | $0 | $703,500 | $5580 |
| Walker, Delanie | TE | 2012 | $1,910,580 | $860,000 | $0 | $0 | $1,045,000 | $5580 |
| Brown, Tarell | CB | 2013 | $1,736,330 | $880,750 | $0 | $0 | $850,000 | $5580 |
| Lee, Andy | P | 2012 | $1,382,248 | $276,668 | $0 | $0 | $1,100,000 | $5580 |
| Kaepernick, Colin | QB | 2014 | $1,170,193 | $556,691 | $0 | $0 | $607,922 | $5580 |
| Jennings, Brian | LS | 2014 | $1,151,580 | $221,000 | $0 | $0 | $925,000 | $5580 |
| Boone, Alex | RT | 2015 | $935,580 | $340,000 | $0 | $50,000 | $540,000 | $5580 |
| Pontbriand, Ryan | LS/ C | 2012 | $930,580 | $0 | $0 | $0 | $925,000 | $5580 |
| Bowman, NaVorro | ILB | 2013 | $721,142 | $175,562 | $0 | $0 | $540,000 | $5580 |
| Jean Francois, Ricky | NT | 2012 | $631,330 | $10,750 | $0 | $0 | $615,000 | $5580 |
| Culliver, Chris | CB | 2014 | $620,299 | $149,719 | $0 | $0 | $465,000 | $5580 |
| Hunter, Kendall | RB | 2014 | $580,385 | $109,805 | $0 | $0 | $465,000 | $5580 |
| Dixon, Anthony | RB | 2013 | $575,730 | $30,150 | $0 | $0 | $540,000 | $5580 |
| Byham, Nate | TE | 2013 | $572,130 | $26,550 | $0 | $0 | $540,000 | $5580 |
| Williams, Kyle | WR | 2013 | $565,430 | $19,850 | $0 | $0 | $540,000 | $5580 |
| Kilgore, Daniel | OG | 2014 | $510,655 | $40,075 | $0 | $0 | $465,000 | $5580 |
| Miller, Bruce | FB | 2014 | $486,193 | $15,613 | $0 | $0 | $465,000 | $5580 |
| Person, Mike | OG | 2014 | $482,055 | $11,475 | $0 | $0 | $465,000 | $5580 |
| Matthews, John | WR | 2013 | $470,850 | $0 | $0 | $0 | $465,000 | $5580 |
| Williams, Ian | NT | 2013 | $470,580 | $0 | $0 | $0 | $465,000 | $5580 |
| Jones, Colin | FS | 2014 | $470,580 | $0 | $0 | $0 | $465,000 | $5580 |
| Dobbs, Demarcus | DE | 2013 | $470,580 | $0 | $0 | $0 | $465,000 | $5580 |
| Tolzien, Scott | QB | 2013 | $470,580 | $0 | $0 | $0 | $465,000 | $5580 |
| Holcomb, Curtis | CB | 2014 | $401,475 | $11,475 | $0 | $0 | $390,000 | $5580 |
| Wilhoite, Michael | OLB | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Wiggins, Kenny | OT | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Bogan, Dontavia | WR | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Chisolm, Garrett | OG | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Hall, Derek | OT | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Hastings, Joe | WR | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Reuland, Konrad | TE | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Nelson, Kyle | LS | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Nelms, Cory | CB | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| LeGree, Mark | FS | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
| Beeler, Chase | C | 2013 | $395,580 | $0 | $0 | $0 | $390,000 | $5580 |
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