Career Passing Yards
*Missing 1991 statistics
Career Passing Touchdowns
*Missing 1991 statistics
| Years | Comp | Att | Yards | ||
| 1. | Brian Senske | 2000-03 | 522 | 925 | 6,780 |
| 2. | Matt Penz | 2004-07 | 406 | 695 | 5,835 |
| 3. | Keith Karpinski* | 1990-93 | 5,078 | ||
| 4. | Jason Wilsey | 2002-05 | 338 | 587 | 4,652 |
| 5. | Chuck Ohm | 1993-96 | 345 | 677 | 4,069 |
| 6. | Joe Hammond | 1998-01 | 230 | 407 | 3,303 |
| 7. | Paul Anderson | 1965-67 | 164 | 354 | 2,429 |
| 8. | Peter Schultz | 1995-98 | 186 | 365 | 2,299 |
| 9. | Chris Novak | 1986-89 | 172 | 436 | 2,293 |
| 10. | Chris Reinerston | 1985-88 | 137 | 320 | 1,784 |
| 11. | Bob Klefsaas | 1978-81 | 125 | 327 | 1,755 |
Career Passing Touchdowns
| Years | Touchdowns | ||
| 1. | Matt Penz | 2004-07 | 51 |
| 2. | Brian Senske | 2000-03 | 45 |
| 3. | Jason Wilsey | 2002-05 | 42 |
| 4. | Chuck Ohm | 1993-96 | 33 |
| 5. | Keith Karpinski* | 1990-93 | 29 |
| 6. | Joe Hammond | 1998-01 | 22 |
| 7. | Paul Anderson | 1965-67 | 20 |
| 8. | Peter Schultz | 1995-98 | 19 |
| 9. | Bob Klefsaas | 1978-81 | 18 |
| 10. | Chris Reinerston | 1985-88 | 11 |
| 11t. | Karl Bowman | 1969-71 | 10 |
| 11t. | Chris Novak | 1986-89 | 10 |

