ACTIVE
| # | Player | Position | College | Acquired |
| 1 | Jacobs, Chuck | WR | 2013-UDFA | |
| 2 | McCoy, Colt | QB | Texas | 2013-T(CLE) |
| 3 | Tolzien, Scott | QB | Wisconsin | 2011-W(SD) |
| 4 | Lee, Andy | P | Pittsburgh | 2004-6th |
| 5 | Daniels, B.J. | QB | South Florida | 2013-7th |
| 6 | Santella, Anthony | P | Illinois | 2013-FA |
| 7 | Kaepernick, Colin | QB | Nevada | 2011-2nd |
| 9 | Dawson, Phil | PK | Texas | 2013-UFA(CLE) |
| 10 | Williams, Kyle | WR | Arizona State | 2010-7th |
| 11 | Patton, Quinton | WR | Louisiana Tech | 2013-4th |
| 13 | Hastings, Joe | WR | Washburn | 2012-FA |
| 14 | Hall, Chad | WR | Air Force | 2013-FA |
| 15 | Crabtree, Michael | WR | Texas Tech | 2009-1st |
| 17 | Jenkins, A.J. | WR | Illinois | 2012-1st |
| 18 | Lockette, Ricardo | WR | Fort Valley State | 2012-FA(SEA) |
| 19 | Moore, Marlon | WR | Fresno State | 2013-FA(MIA) |
| 20 | Cox, Perrish | CB | Oklahoma State | 2012-FA(DEN) |
| 21 | Gore, Frank | RB | Miami(Fla.) | 2005-3rd |
| 22 | Rogers, Carlos | CB | Auburn | 2011-UFA(WAS) |
| 23 | James, LaMichael | RB | Oregon | 2012-2nd |
| 24 | Asomugha, Nnamdi | CB | California | 2013-FA(PHI) |
| 24 | Dixon, Anthony | RB | Mississippi State | 2010-6th |
| 25 | Brown, Tarell | CB | Texas | 2007-5th |
| 26 | Brock, Tramaine | CB | Belhaven | |
| 27 | Spillman, C.J. | FS | Marshall | 2009-W(SD) |
| 28 | McBath, Darcel | SS | Texas Tech | 2012-FA(DEN) |
| 29 | Culliver, Chris | CB | South Carolina | 2011-3rd |
| 30 | Robinson, Trenton | SS | Michigan State | 2012-6th |
| 31 | Whitner, Donte | SS | Ohio State | 2011-UFA(BUF) |
| 32 | Hunter, Kendall | RB | Oklahoma State | 2011-4th |
| 33 | Cooper, Marcus | CB | Rutgers | 2013-7th |
| 33 | Hampton, Jewel | RB | Southern Illinois | 2012-UDFA |
| 35 | Reid, Eric | FS | LSU | 2013-1st |
| 36 | Harper, D.J. | RB | Boise State | 2013-UDFA |
| 36 | Thomas, Michael | FS | Stanford | 2012-UDFA |
| 38 | Morris, Darryl | CB | Texas State | 2013-UDFA |
| 38 | Lattimore, Marcus | RB | South Carolina | 2013-4th |
| 40 | Rose, Lowell | CB | Tulsa | 2013-UDFA |
| 43 | Dahl, Craig | FS | North Dakota State | 2013-UFA(STL) |
| 44 | Debniak, Alex | FB | Stanford | 2013-UDFA |
| 45 | Stupar, Nate | OLB | Penn State | 2012-FA |
| 46 | Gray, MarQuies | RB | Minnesota | 2013-UDFA |
| 47 | McDermott, Kevin | LS | UCLA | 2013-UDFA |
| 48 | Tukuafu, Will | FB/DE | Oregon | 2012-FA |
| 49 | Miller, Bruce | FB | Central Florida | 2011-7th |
| 50 | Johnson, Cam | OLB | Virginia | 2012-7th |
| 51 | Skuta, Dan | ILB | Grand Valley State | 2013-UFA(CIN) |
| 52 | Willis, Patrick | ILB | Ole Miss. | 2007-1st |
| 53 | Bowman, NaVorro | ILB | Penn State | 2010-3rd |
| 54 | Moody, Nick | ILB | Florida State | 2013-6th |
| 55 | Brooks, Ahmad | OLB | Virginia | 2008-W(CIN) |
| 57 | Wilhoite, Michael | ILB | Washburn | 2011-FA |
| 58 | Fleming, Darius | OLB | Notre Dame | 2012-5th |
| 59 | Goodwin, Jonathan | C | Michigan | 2011-UFA(NO) |
| 60 | Carter, Sherman | C | Tennessee State | 2013-UDFA |
| 62 | Tribue, Wayne | OG | Temple | 2013-FA |
| 63 | Jerod-Eddie, Tony | DE | Texas A&M | 2012-UDFA |
| 64 | Marquardt, Luke | OT | Azusa Pacific | 2013-UDFA |
| 64 | Purcell, Michael | NT | Wyoming | 2013-UDFA |
| 65 | Netter, Al | LT/OG | Northwestern | 2012-UDFA |
| 66 | Omameh, Patrick | OG | Michigan | 2013-UDFA |
| 67 | Kilgore, Daniel | C | Appalachian State | 2011-5th |
| 68 | Snyder, Adam | OG/OT | Oregon | 2005-3rd |
| 69 | Wiggins, Kenny | RT/OG | Fresno State | 2011-FA |
| 71 | Bykowski, Carter | OT | Iowa State | 2013-7th |
| 71 | Dial, Quinton | DE | Alabama | 2013-5th |
| 74 | Staley, Joe | LT | Central Michigan | 2007-1st |
| 75 | Boone, Alex | RG | Ohio State | 2009-UDFA |
| 76 | Davis, Anthony | RT | Rutgers | 2010-1st |
| 77 | Iupati, Mike | LG | Idaho | 2010-1st |
| 78 | Okoye, Lawrence | DE | Britian | 2013-UDFA |
| 78 | Looney, Joe | LG/C | Wake Forest | 2012-4th |
| 81 | Boldin, Anquan | WR | Florida State | 2013-T(BAL) |
| 82 | Manningham, Mario | WR | Michigan | 2012-UFA(NYG) |
| 83 | Dobbs, Demarcus | TE/DE | Georgia | 2011-UDFA |
| 84 | Morrah, Cameron | TE | California | 2013-FA(SEA) |
| 85 | Davis, Vernon | TE | Maryland | 2006-1st |
| 86 | Jennings, Brian | LS | Arizona State | 2000-7th |
| 88 | Celek, Garrett | TE | Michigan State | 2012-UDFA |
| 89 | McDonald, Vance | TE | Rice | 2013-3rd |
| 90 | Dorsey, Glenn | NT/DE | LSU | 2013-UFA(KC) |
| 91 | McDonald, Ray | DE | Florida | 2007-3rd |
| 92 | Divens, Lamar | NT | Tennessee State | 2012-FA |
| 93 | Williams, Ian | NT | Notre Dame | 2011-UDFA |
| 94 | Smith, Justin | DE | Missouri | 2008-UFA(CIN) |
| 95 | Carradine, Tank | DE | Florida State | 2013-2nd |
| 96 | Lemonier, Corey | OLB | Auburn | 2013-3rd |
| 98 | Haralson, Parys | OLB | Tennessee | 2006-6th |
| 99 | Smith, Aldon | OLB | Missouri | 2011-1st |
