| 2011 |
| 1 | 7 | Aldon Smith | DE | 6-4 | 263 | Missouri |
| 2 | 4 | Colin Kaepernick | QB | 6-5 | 233 | Nevada |
| 3 | 16 | Chris Culliver | S | 6-0 | 199 | South Carolina |
| 4 | 18 | Kendall Hunter | RB | 5-7 | 199 | Oklahoma State |
| 5 | 32 | Daniel Kilgore | G | 6-3 | 308 | Appalachian State |
| 6 | 17 | Ronald Johnson | WR | 5-11 | 199 | USC |
| 6 | 25 | Colin Jones | S | 6-0 | 208 | TCU |
| 7 | 8 | Bruce Miller | OLB | 6-1 | 254 | UCF |
| 7 | 38 | Mike Person | T | 6-5 | 299 | Montana State |
| 7 | 49 | Curtis Holcomb | CB | 5-10 | 190 | Florida A&M |
| 2010 |
| 1 | 11 | Anthony Davis | T | 6-5 | 323 | Rutgers |
| 1 | 17 | Mike Iupati | G | 6-5 | 331 | Idaho |
| 2 | 17 | Taylor Mays | S | 6-3 | 230 | USC |
| 3 | 27 | Navorro Bowman | OLB | 6-1 | 242 | Penn State |
| 6 | 4 | Anthony Dixon | RB | 6-1 | 233 | Mississippi State |
| 6 | 13 | Nate Byham | TE | 6-4 | 268 | Pittsburgh |
| 6 | 37 | Kyle Williams | WR | 5-10 | 188 | Arizona State |
| 7 | 17 | Phillip Adams | CB | 5-10 | 192 | South Carolina State |
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