Boise State played Hawaii for the first time in 1996 in the middle of the worst season in Boise State history. This was Boise State's first year of Division 1A football joining the Big West conference after 26 seasons in the Big Sky Conference. Head Coach Pokey Allen resigned prior to the start of the season to battle his life-threatening cancer full time. Interim Coach Tom Mason did not have full support of his staff or players and it showed on the field. The Tony Hilde led Broncos played with a lot of heart, but lost to the Warriors of the Western Athletic Conference 20 to 14. Ironically, both Boise State and Hawaii would finish their seasons with identical 2-10 records.
The Broncos of the Big West Conference would play Hawaii again in 1999. The 1999 Bronco team was led by quarterback Bart Hendricks and was a much-improved team under Head Coach Dirk Koetter. The 1999 Bronco team would finish with a 10-3 record, a Big West Conference Championship and a win over Louisville in the Humanitarian Bowl. But one of their 3 losses would be to Hawaii. After leading 19 to 7 at half-time, the favored Broncos would not score in the second half and lose 34 to 7. It would be Hawaii's first win over a Division 1A team in 2 years. The 1998 Hawaii team finished 0-11, which led Hawaii to make a coaching change. Hawaii hired June Jones who coached Hawaii to the biggest one-year turnaround in Division 1A football history. Hawaii would finish with a 9-4 record and Coach Jones would win the TSN Coach of the Year Award.
The next time Hawaii and Boise State would play football, it would be in a Western Athletic Conference game. Boise State joined the WAC in 2001 and played their third game versus Hawaii in Hawaii again. This time, the Broncos would win the game 28 to 21 with first year Head Football Coach Dan Hawkins and sophomore quarterback Ryan Dinwiddie at the helm.
Hawaii finally visited Bronco Stadium in 2002. Hawaii and Fresno State were the preseason favorites to win the WAC football championship. This was a huge game for the Broncos and it was homecoming. Broncos need to win badly to prove that they were contenders for the WAC Championship. Hawaii came into the game favored with only a 3-point loss to BYU on their record. The Broncos had something to prove and they did it in the Hawaii game winning handily 58 to 31 and going on the win their first WAC championship. It would be Hawaii's only WAC loss and it would cost Hawaii a WAC Championship.
The Defending WAC Champion Broncos had to travel to Hawaii in 2003 to face a June Jones Hawaii team that was out for revenge. In 2002, Hawaii had 3 regular season losses. They lost to BYU by 3 points. They lost to Alabama by 5 points. They lost to Boise State by 27 points. Timmy Chang, the Hawaii quarterback, was leading the nation in passing and Hawaii was scoring a lot of points. For some reason, Timmy Chang did not play in the first half against the Broncos. He was inserted in the 3rd quarter of the game, but the Broncos would shut down Chang and win the game 45 to 28. Only USC would beat Hawaii by more points in 2003.Boise State would go on to win back to back WAC Championships in 2003.
The 2004 Boise State/Hawaii match up was a big ESPN game in Bronco Stadium with Timmy Chang closing in on Ty Detmer's all time Division 1A career passing yards record. Timmy Chang did set an all time career record that night in Boise, Idaho, but it was not the one he wanted. Chang was intercepted 4 times by the Bronco secondary and set a record for most interceptions in NCAA history with 74, surpassing the mark held by Purdue's Mark Herrmann. Hawaii scored first on a field goal and led 3 to 0. The Broncos scored the next 69 points and Hawaii lost 69 to 3. The Broncos would go on to finish undefeated in WAC play for their third consecutive WAC championship.