Meierkort began his coaching career at Dakota Wesleyan, where he also served as head baseball coach. From there he served as a graduate assistant at South Dakota State before moving on to Southwest Minnesota State University, where he held various positions from 1983 to 1993.
Meierkort was named head coach of the Coyotes in 2004. He has overseen the program's elevation from the NCAA Division II rank to Division I. The team's first victory against a Division I opponent came against the Southern Utah Thunderbirds of the FCS on November 15, 2008. In 2010, the program achieved its first win against an FBS opponent with a victory over the Minnesota Golden Gophers. In his last game as South Dakota's coach his team blew a 20 point halftime lead against the University of North Dakota Fighting Sioux.