Kustra said in a statement Boise State has successfully worked out a deal to remain one of the anchors of the conference.
"I am confident that our Mountain West membership is the very best decision for Boise State University, our student-athletes and our incredible fan base," he said.
"Maintaining the Broncos program as part of the already solid foundation we have established creates a posture of great stability for the Mountain West going forward," MWC Commissioner Craig Thompson added.
Boise State was set to join the beleaguered Big East in football only starting next season but reconsidered its options when Rutgers defected to the Big 12 and Louisville opted for the Atlantic Coast Conference.
The Broncos were planning on joining the Big West for other sports, but now will stay in the MWC for all its athletic programs.
With Boise State's decision, the Big East has now lost 14 existing or future members over the past two years.