In 1997, Henson returned to New Mexico State as interim head coach after Neil McCarthy was abruptly fired before the start of the season. Henson wanted to donate his time, but was told that state law didn't allow him to coach for free. He finally accepted a nominal salary of $1 per month. After a successful season, he was given his old job back on a permanent basis. His 1998–99 team won the Big West regular season and tournament titles—notably, the first time in Henson's career that he had won a conference tournament. He retired for good midway through the 2004–05 season due to non-Hodgkin's lymphoma. His second stint allowed him to regain his standing as New Mexico State's all-time winningest coach, passing McCarthy.