| Game Date |
| Opponent | Conference Game | Result | Commentary |
| 2/2/2006 | at | Texas-Pan American |
| L 8-3 |
|
| 2/3/2006 | vs | Lamar |
| W 7-6 | UTPA Classic, Edinburg, TX |
| 2/4/2006 | vs | Texas State |
| W 8-4 | UTPA Classic, Edinburg, TX |
| 2/5/2006 | vs | Northern Colorado |
| W 12-5 | UTPA Classic, Edinburg, TX |
| 2/10/2006 | vs | Arizona State |
| W 9-1 | Coca-Cola Classic, Surprise, AZ |
| 2/11/2006 | vs | Nevada |
| W 11-5 | Coca-Cola Classic, Surprise, AZ |
| 2/12/2006 | vs | Oregon State |
| W 6-5 | Coca-Cola Classic, Surprise, AZ |
| 2/17/2006 | at | New Mexico State |
| L 5-3 |
|
| 2/18/2006 | at | New Mexico State |
| W 14-4 |
|
| 2/19/2006 | at | New Mexico State |
| L 10-8 |
|
| 2/24/2006 | at | Washington |
| L 14-4 |
|
| 2/25/2006 | at | Washington |
| L 8-6 |
|
| 2/26/2006 | at | Washington |
| L 7-5 |
|
| 3/2/2006 | at | Lewis-Clark State |
| | Banana Belt Tournament, Lewiston, ID (played under NAIA rules, 8-7 Gonzaga win doesn't count) |
| 3/3/2006 | vs | Washington State |
| L 18-10 | Banana Belt Tournament, Lewiston, ID |
| 3/4/2006 | vs | Chicago State |
| W 22-4 | Banana Belt Tournament, Lewiston, ID |
| 3/5/2006 | at | Washington State |
| W 7-0 | Banana Belt Tournament, Pullman, WA |
| 3/10/2006 |
| Chicago State |
| W 6-0 |
|
| 3/11/2006 |
| Chicago State |
| W 12-4 |
|
| 3/13/2006 | vs | Miami, Ohio |
| L 4-1 | Pepsi/Johnny Quik Classic, Fresno, CA |
| 3/14/2006 | at | Fresno State |
| L 5-1 | Pepsi/Johnny Quik Classic, Fresno, CA |
| 3/15/2006 | vs | Bucknell |
| W 12-2 | Pepsi/Johnny Quik Classic, Fresno, CA |
| 3/16/2006 | vs | Lafayette |
| W 6-3 | Pepsi/Johnny Quik Classic, Fresno, CA |
| 3/17/2006 | vs | Washington State |
|
| PPD, rain (Pepsi/Johnny Quik Classic, Fresno, CA) |
| 3/18/2006 | vs | Washington State |
| L 15-3 | Pepsi/Johnny Quik Classic, Fresno, CA (makeup of 3/17 game) |
| 3/18/2006 | vs | Binghamton |
| W 12-1 | Pepsi/Johnny Quik Classic, Fresno, CA |
| 3/24/2006 |
| Dartmouth |
| W 14-7 |
|
| 3/25/2006 |
| Dartmouth |
|
| CCD, rain |
| 3/26/2006 |
| Dartmouth |
| W 13-2 |
|
| 3/28/2006 |
| Whitworth |
| W 6-1 |
|
| 3/31/2006 |
| Portland | * | W 8-7 | 10 innings |
| 4/1/2006 |
| Portland | * | W 4-3 |
|
| 4/2/2006 |
| Portland | * | W 5-4 |
|
| 4/4/2006 | at | Washington State |
| W 6-2 | Gonzaga turns 2 triple plays |
| 4/7/2006 |
| Santa Clara | * | W 5-1 |
|
| 4/8/2006 |
| Santa Clara | * | L 7-6 |
|
| 4/9/2006 |
| Santa Clara | * |
| PPD to 4/10, field conditions |
| 4/10/2006 |
| Santa Clara | * | L 8-7 | makeup of 4/9 game |
| 4/15/2006 | at | St. Mary's | * | L 8-4 |
|
| 4/15/2006 | at | St. Mary's | * | L 4-2 | moved from 4/14, field conditions |
| 4/17/2006 | at | St. Mary's | * | W 3-2 | moved from 4/17 |
| 4/18/2006 | at | Washington State |
| W 9-4 |
|
| 4/21/2006 |
| San Francisco | * | W 3-1 |
|
| 4/22/2006 |
| San Francisco | * | L 8-1 |
|
| 4/23/2006 |
| San Francisco | * | W 9-8 |
|
| 4/25/2006 |
| Washington State |
| L 9-6 |
|
| 4/28/2006 | at | Loyola Marymount | * | L 4-3 |
|
| 4/29/2006 | at | Loyola Marymount | * | L 6-3 |
|
| 4/30/2006 | at | Loyola Marymount | * | L 5-0 |
|
| 5/5/2006 |
| Pepperdine | * | W 6-1 |
|
| 5/6/2006 |
| Pepperdine | * | L 13-4 |
|
| 5/7/2006 |
| Pepperdine | * | L 10-4 |
|
| 5/12/2006 | at | San Diego | * | W 7-5 |
|
| 5/13/2006 | at | San Diego | * | L 11-7 |
|
| 5/14/2006 | at | San Diego | * | L 14-4 |
|
| 5/16/2006 |
| Washington State |
| L 11-5 |
|
| 5/18/2006 |
| Lewis-Clark State |
| W 8-1 |
|