McInerney was 48-41 during his tenure, but the Blue Devils were just 4-8 this season.
He said he believes this is a good time to "move onward in my career."
McInerney's 48 wins are second-most in program history, and his teams won a pair of Northeast Conference championships in 2009 and '10. He was named the conference's coach of the year in 2009.
McInerney spent two seasons as the defensive coordinator at Rhode Island before being hired at Central in 2006. He has also been an assistant at Tulsa, UNLV, Oregon State, Georgia Southern and Southern California.
The school says there will be a national search for a successor.