Athletic director Clint Bryant said a national search will begin for a new head coach.
Cooper, a former Augusta State first baseman, went 64-126 during his tenure.
In 2011, Cooper guided the Jaguars to the championship game of the Peach Belt Tournament, a 2-1 loss to No. 10 UNC Pembroke.
“We got the opportunity to do what no other (Augusta State) team has done and play for a Peach Belt championship. That was a highlight,” he said. “I’ve got nothing but good things to say about this program.”
Cooper, who obtained his bachelor’s and masters degrees from Augusta State, will remain at the school, becoming the first full-time head strength and conditioning coach for athletics. He also will continue to teach four classes a semester.
“Augusta State is part of my family,” Cooper said. “I’ve played there. I’ve graduated from there. For 13 years, it’s been a big part of me.”
Augusta State lost staff ace Scott Shipman (1.80 in 2011) to a season-ending shoulder injury in preseason.
The Jaguars went on to post the worst season in Peach Belt history, finishing with a 10-37 overall mark (3-24 conference). The Jaguars closed with a 21-game losing streak – the longest in league history.
Augusta State finished last in the league in hitting (.256) and pitching (5.90 ERA).
“This season was extremely difficult,” Cooper said. “Unfortunately, we came out on the wrong end this year.”