The 1988 baseball team was the first Comets baseball team to win 30 games in a season, finishing with a record of 30-9. The team had a perfect 16-0 conference record in the NDCAC and won the conference tournament. They advanced to the NAIA Area III Tournament in North Platte, Neb., and in the first game of the tournament, defeated Kearney State in one of the greatest come-from-behind wins in Mayville State history. Five members of the team, Hoffner, Roaldson, Reidy, Schwabe, and Booker, hit .400 and higher and Hoffner hit .519. Two pitchers, Matsubara and Biberdorf, had a combined record of 18-1. Hoffner, Reidy, Roaldson, Biberdorf, Matsubara, and Booker were named to the all-district team. Biberdorf was named the District 12 Player of the Year. Biberdorf and Hoffner were named NAIA All-Americans. They were drafted by Major League Baseball organizations and played in the minor leagues. Schwabe and Matsubara played on the Canadian National Team.
Head coach of the 1988 baseball team was Scott Berry. He was assisted by Dave Wheeler. Members of the team were Lane Curry, Jamie Hoffner, Cam Biberdorf, Paul Hanson, Gary Powell, Chuck Bush, Dennis Reidy, Terry Magnuson, Scott Whetter, Shaun Cory, Joey Mutcheson, Jason Schwabe, Darren Thompson, Kevin Booker, Mike Kolness, Tom Rothmann, Todd Martin, Jim Roaldson, Steve Boe, Gerry Smith, and Fred Matsubara.