Houston, 44, succeeds Everett Withers, who departed Jan. 6 to take over at Texas State. He will be introduced at a news conference on campus Tuesday.
"I am thrilled to welcome Mike Houston as the next football head coach at James Madison," athletic director Jeff Bourne said. "Mike has been a fast riser in the coaching ranks with success turning programs around at the Division II and FCS levels. His pedigree for winning and ability to lead young men make him the perfect fit to build upon the foundation already in place at JMU."
Houston, the seventh coach in JMU history, is 43-19 in five seasons in college.
He ran a triple-option offense at The Citadel, where he went 14-11 in two years, including 9-4 this past season when he led the Bulldogs to a share of the Southern Conference title and their first FCS playoff appearance since 1992. They beat Coastal Carolina in a Nov. 28 playoff game one week after finishing the regular season with a 23-22 upset of SEC member South Carolina.
"After being approached about the job at James Madison, the more research I did and the more people I met there, it became obvious to me that this was a fantastic opportunity," Houston said. "The Citadel will always be a special place because of the relationships my family and I developed, and I wish the cadet-athletes, coaches and staff the best moving forward."
Houston, a 1994 Mars Hill graduate, went 29-8 at Division II Lenoir-Rhyne, winning the South Atlantic Conference title in each of his three seasons from 2011-13. In his final year, the Bears advanced to the Division II national championship game.
Withers went 18-7 in two years at James Madison, including a share of the CAA Football title this past season. But the Dukes lost their first playoff game at home in both seasons - a disappointment for a program that has aspirations of moving up to the FBS level in the future.
Withers left behind a JMU team that returns one of the leading offenses in the FCS as well as four all-CAA first-team selections.
JMU has ranked in the top five of the FCS for attendance in each of the last five seasons.