Stein was a graduate assistant and coach for Central Michigan University, where she earned a master's degree in physical education with an emphasis in athletic administration. After jobs as an assistant coach at Miami University, the University of Cincinnati, and Bradley University, Stein returned to her alma mater, first as a recruiting coach, and then as an assistant coach for her former team.
Her first head coaching assignment came at Emporia State University, an NCAA Division II school in Emporia, Kansas. In three years as head coach at Emporia State, Stein turned the women's basketball program into a national contender, with her team advancing to the NCAA Division II title game in 1998. This success earned Stein various coaching awards, including being named the Division II Basketball coach of the year.
Stein coached for 12 seasons Missouri. She compiled a 185–177 career mark at Missouri from 1998 to 2010. She led the Tigers to two NCAA tournament berths, including a 2001 Sweet 16 appearance. She has had 29 selections to the Academic All Big 12 teams. In the Big 12 Conference, she guided the Tigers to multiple seasons above .500 in league play. She announced her resignation, effective at the end of the 2009–10 season, on her radio show on March 1, 2010.
Stein was a TV analyst for Fox Sports basketball games. From 2010 to 2012 she provided color commentary for UMKC women's basketball along with play-by-play broadcaster T. J. Jackson on KCWJ.