The announcement was made Tuesday by athletic director Mike Jones.
Jones says a search committee would be appointed to find Joseph’s successor. The school joins the Gulf South Conference next season.
Joseph became the Choctaws’ coach in 2004 and led them to a 9-3 record and the American Southwest Conference championship in 2009.
Mississippi College was 4-6 this year. It finished the season with a 56-30 loss to second-ranked Mary Hardin-Baylor on Saturday. Joseph coached also for three seasons at Belhaven, from 1998-2000 and has a career record of 63-70 as a head coach.
He has also had stints as the offensive coordinator at Southern Miss, Louisiana-Monroe and San Jose State.