| Day | Date | Opponent | Location | TV | Outcome/Time |
| Mon | 11/15/1999 | Basketball Travelers | San Diego
(Exhibition) | | 7:00 PM PT
|
| Mon | 11/22/1999 | EA Sports All-Stars | San Diego
(Exhibition) | | 7:00 PM PT
|
| Wed | 11/24/1999 | UC Riverside | San Diego
(Kids Free-Static Sticker Giveaway) | | W, 73-57
Recap | Archived Audio |
| Tue | 11/30/1999 | New Mexico State | Las Cruces, N.M. | | L, 66-49
Recap | Stats | Archived Audio |
| Sat | 12/04/1999 | USD | San Diego
(USD) | | L, 73-45
Recap | Stats | Archived Audio |
| Sun | 12/12/1999 | Oklahoma State | Oklahoma City, Okla | | L, 97-63
Recap | Stats |
| Thu | 12/16/1999 | South Carolina State | San Diego
(Kids Free) | | W, 72-57
Recap | Stats | Archived Audio |
| Sat | 12/18/1999 | ASU | Tempe, Ariz. | | L, 99-85
Recap | Stats | Archived Audio |
| Mon | 12/20/1999 | USC | San Diego
(Kids Free) | | L, 87-54
Recap | Stats | Archived Audio |
| Wed | 12/22/1999 | UCSB | San Diego
(Kids Free) | | W, 60-57
Recap | Stats | Archived Audio |
| Mon | 12/27/1999 | Ball State | San Diego
(Kids Free) | | L, 82-65
Recap | Archived Audio |
| Thu | 12/30/1999 | Loyola Marymount | San Diego
(Kids Free) | | W, 70-63
Recap | Stats | Archived Audio |
| Sun | 01/02/2000 | High Point | San Diego
(Kids Free) | | W, 74-63
Recap | Stats |
| Wed | 01/05/2000 | CSU-Fullerton | San Diego
(kids Free) | | L, 72-66
Recap | Stats | Archived Audio |
| Sat | 01/08/2000 | Pacific | Stockton, Calif. | | L, 74-63
Recap | Stats | Archived Audio |
| Mon | 01/10/2000 | Utah* | San Diego | | L, 70-55
Recap | Stats | Archived Audio |
| Thu | 01/20/2000 | Air Force* | San Diego | | L, 81-77, 3OT
Recap | Stats | Archived Audio |
| Sat | 01/22/2000 | UNLV* | Las Vegas | | L, 83-55
Recap | Stats | Archived Audio |
| Thu | 01/27/2000 | Colorado State* | Fort Collins, Colo. | | L, 75-67
Recap | Archived Audio |
| Sat | 01/29/2000 | Wyoming* | Laramie, Wyo. | | L, 93-87
Recap | Stats | Archived Audio |
| Thu | 02/03/2000 | BYU* | San Diego | | L, 72-50
Recap | Stats | Archived Audio |
| Sat | 02/05/2000 | New Mexico* | San Diego
(Free Sports Bottle Night) | | L, 78-57
Recap | Stats | Archived Audio |
| Thu | 02/10/2000 | Utah* | Salt Lake City | | L, 83-65
Recap | Stats | Archived Audio |
| Sat | 02/12/2000 | Colorado State* | San Diego
(U-T Youth & Family) | | L, 74-46
Recap | Stats | Archived Audio |
| Sat | 02/19/2000 | Wyoming* | San Diego
(U-T Youth & Family) | | L, 71-57
Recap | Stats | Archived Audio |
| Thu | 02/24/2000 | Air Force* | Colorado Springs, Colo. | | L, 63-55
Recap | Stats | Archived Audio |
| Sat | 02/26/2000 | New Mexico* | Albuquerque, N.M. | | L, 78-49
Recap | Stats | Archived Audio |
| Thu | 03/02/2000 | UNLV* | San Diego | | L, 85-64
Recap | Stats | Archived Audio |
| Sat | 03/04/2000 | BYU* | Provo, Utah | | L, 67-50
Recap | Archived Audio |
| Thu | 03/09/2000 | UNLV (Mountain West Conference Tournament) | Las Vegas
(Thomas & Mack Center) | | L, 77-72
Recap | Stats | Archived Audio |
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