"Last evening, Coach Houston informed us that he had interest in exploring other head coaching opportunities, while remaining under consideration here," Charlotte athletic director Mike Hill said in a statement. "We feel great about our candidate pool and believe this institution, our students, fans and team deserve a head coach that is 100 percent committed to the Charlotte 49ers."
James Madison's season has yet to end. The Dukes face Colgate on Saturday in the second round of the FCS playoffs.
Houston, 47, is 37-5 at James Madison with an FCS national title in 2016 and a runner-up finish last season. He previously coached at The Citadel and Lenoir-Rhyne, boasting an 80-24 overall record as a college head coach.
Charlotte is looking to replace Brad Lambert, who was fired Nov. 18 following six seasons where he went 21-48 in the program's first six years of existence.