After taking over a winless program in June of 2007 Allen led SBU to a 5 win season in 2008 before posting its first winning record since 2001 in 2009. The Bearcats went 7-4 and 6-5 respectively over the next two seasons while playing a non-conference D-2 schedule.
Allen's previous coaching stops include Oklahoma, NE Louisiana, Texas Christian, Quincy and San Jose State.
"I would like to thank Coach Allen for his service and laying a foundation which will give our next head coach an opportunity to take our program to the next level," SBU Director of Athletics Mike Pitts said in a statement.
Pitts will immediately form a search committee, which he will chair, which will quickly launch a nationwide search for candidates.