| 2008 |
| 1 | 29 | Kentwan Balmer | DT | 6-5 | 298 | North Carolina |
| 2 | 8 | Chilo Rachal | G | 6-5 | 315 | Southern California |
| 3 | 12 | Reggie Smith | CB | 6-1 | 198 | Oklahoma |
| 4 | 8 | Cody Wallace | C | 6-4 | 298 | Texas A&M |
| 6 | 8 | Josh Morgan | WR | 6-1 | 215 | Virginia Tech |
| 7 | 7 | Larry Grant | OLB | 6-1 | 232 | Ohio State |
| 2007 |
| 1 | 11 | Patrick Willis | ILB | 6-1 | 240 | Mississippi |
| 1 | 28 | Joe Staley | OT | 6-6 | 306 | Central Michigan |
| 3 | 12 | Jason Hill | WR | 6-0 | 210 | Washington State |
| 3 | 34 | Ray McDonald | DT | 6-3 | 276 | Florida |
| 4 | 5 | Jay Moore | DE/OLB | 6-5 | 276 | Nebraska |
| 4 | 27 | Dashon Goldson | FS | 6-2 | 202 | Washington |
| 4 | 36 | Joe Cohen | DT | 6-2 | 313 | Florida |
| 5 | 10 | Tarell Brown | CB | 5-11 | 192 | Texas |
| 6 | 12 | Thomas Clayton | RB | 5-10 | 218 | Kansas State |
| 2006 |
| 1 | 6 | Vernon Davis | TE | 6-3 | 256 | Maryland |
| 1 | 22 | Manny Lawson | OLB | 6-5 | 241 | North Carolina State |
| 3 | 20 | Brandon Williams | WR | 5-9 | 180 | Wisconsin |
| 4 | 3 | Michaeil Robinson | WR | 6-1 | 226 | Penn State |
| 5 | 7 | Parys Haralson | DE | 6-1 | 253 | Tennessee |
| 6 | 6 | Delanie Walker | WR | 6-1 | 240 | Central Missouri State |
| 6 | 23 | Marcus Hudson | FS | 6-1 | 195 | North Carolina State |
| 6 | 28 | Melvin Oliver | DE | 6-3 | 279 | Louisiana State |
| 7 | 46 | Vickiel Vaughn | FS | 5-11 | 208 | Arkansas |
| 2005 |
| 1 | 1 | Alex Smith | QB | 6-4 | 217 | Utah |
| 2 | 1 | David Baas | C/G | 6-4 | 319 | Michigan |
| 3 | 1 | Frank Gore | RB | 5-9 | 212 | Miami (FL) |
| 3 | 31 | Adam Snyder | G | 6-5 | 316 | Oregon |
| 5 | 1 | Ronald Fields | NG | 6-2 | 313 | Mississippi St. |
| 5 | 38 | Rasheed Marshall | WR | 5-11 | 185 | West Virginia |
| 6 | 31 | Derrick Johnson | CB | 5-11 | 197 | Washington |
| 7 | 1 | Daven Holly | CB | 5-10 | 192 | Cincinnati |
| 7 | 9 | Marcus Maxwell | WR | 6-4 | 205 | Oregon |
| 7 | 34 | Patrick Estes | TE | 6-6 | 280 | Virginia |
| 7 | 35 | Billy Bajema | TE | 6-5 | 261 | Oklahoma St. |
| 2004 |
| 1 | 31 | Rashaun Woods | WR | 6-2 | 202 | Oklahoma State |
| 2 | 14 | Justin Smiley | G | 6-3 | 301 | Alabama |
| 2 | 26 | Shawntae Spencer | CB | 6-0 | 176 | Pittsburgh |
| 3 | 14 | Derrick Hamilton | WR | 6-3 | 203 | Clemson |
| 4 | 8 | Isaac Sopoaga | NG/DT | 6-2 | 321 | Hawaii |
| 4 | 31 | Richard Seigler | LB | 6-2 | 238 | Oregon State |
| 6 | 23 | Andy Lee | P | 6-0 | 206 | Pittsburgh |
| 6 | 33 | Keith Lewis | FS | 6-0 | 202 | Oregon |
| 7 | 16 | Cody Pickett | QB | 6-3 | 227 | Washington |
| 7 | 25 | Christian Ferrara | DT | 6-3 | 294 | Syracuse |
| 2003 |
| 1 | 26 | Kwame Harris | T | 6-7 | 310 | Stanford |
| 2 | 25 | Anthony Adams | DT | 6-0 | 300 | Penn State |
| 3 | 25 | Andrew Williams | DE | 6-2 | 263 | Miami |
| 4 | 27 | Brandon Lloyd | WR | 6-0 | 184 | Illinois |
| 5 | 26 | Aaron Walker | TE | 6-6 | 252 | Florida |
| 6 | 24 | Arnaz Battle | WR | 6-0 | 217 | Notre Dame |
| 7 | 27 | Ken Dorsey | QB | 6-4 | 205 | Miami |
| 2002 |
| 1 | 27 | Mike Rumph | CB | 6-2 | 205 | Miami (FL) |
| 3 | 4 | Saleem Rasheed | LB | 6-2 | 229 | Alabama |
| 4 | 4 | Jeff Chandler | K | 6-2 | 218 | Florida |
| 4 | 29 | Kevin Curtis | S | 6-2 | 212 | Texas Tech |
| 5 | 28 | Brandon Doman | QB | 6-1 | 210 | BYU |
| 5 | 37 | Josh Shaw | DT | 6-2 | 279 | Michigan State |
| 6 | 29 | Mark Anelli | TE | 6-3 | 265 | Wisconsin |
| 7 | 28 | Eric Heitmann | G | 6-3 | 305 | Stanford |
| 7 | 38 | Kyle Kosier | T | 6-5 | 293 | Arizona State |
| 7 | 45 | Teddy Gaines | CB | 5-11 | 165 | Tennessee |
| 2001 |
| 1 | 7 | Andre Carter | DE | 6-4 | 265 | California |
| 2 | 16 | Jamie Winborn | LB | 5-11 | 224 | Vanderbilt |
| 3 | 18 | Kevan Barlow | RB | 6-1 | 238 | Pittsburgh |
| 6 | 6 | Cedrick Wilson | WR | 5-10 | 179 | Tennessee |
| 6 | 16 | Rashad Holman | CB | 5-10 | 191 | Louisville |
| 6 | 28 | Menson Holloway | DE | 6-2 | 284 | Texas-El Paso |
| 7 | 9 | Alex Lincoln | LB | 6-0 | 251 | Auburn |
| 7 | 24 | Eric Johnson | TE | 6-3 | 256 | Yale |
| 2000 |
| 1 | 16 | Julian Peterson | LB | 6-3 | 235 | Michigan State |
| 1 | 24 | Ahmed Plummer | CB | 5-11 | 191 | Ohio State |
| 2 | 4 | John Engelberger | DE | 6-4 | 260 | Virginia Tech |
| 2 | 17 | Jason Webster | CB | 5-9 | 180 | Texas A&M |
| 3 | 3 | Giovanni Carmazzi | QB | 6-3 | 224 | Hofstra |
| 3 | 24 | Jeff Ulbrich | LB | 6-0 | 249 | Hawaii |
| 4 | 14 | John Keith | S | 6-0 | 207 | Furman |
| 5 | 3 | Paul Smith | RB | 5-11 | 234 | UTEP |
| 5 | 21 | John Milem | DE | 6-7 | 290 | Lenoir-Rhyne |
| 7 | 6 | Tim Rattay | QB | 6-0 | 215 | Louisiana Tech |
| 7 | 24 | Brian Jennings | TE | 6-5 | 238 | Arizona State |
|
|
|
|
