Huggins, 53, leaves the Big 12 school after only one season to return to his hometown, Morgantown.
KSU was 23-12 (10-6 Big 12) this past season, and played in the NIT.
Huggins played two years at West Virginia and began his coaching career there as a graduate assistant, graduating in 1977 and receiving a master's degree in 1978.
He will assume a program that was guided by John Beilein for the past five years. Beilein was hired by Michigan on Tuesday.
For 15 seasons, Huggins was the head coach at Cincinnati, where he earned 14 NCAA Tournament berths. He was forced out at Cincinnati after numerous brushes with the law by his players, and his own drunken driving arrest in 2004.
He is set to get his 600th career coaching victory next season.