The women's program started with the 1998-99 season after playing as a joint team with the St. Catherine Wildcats for the 1997-98 season. The team has won or shared 4 regular season MIAC titles and 5 conference tournament titles and made 5 NCAA tournament appearances.
The university imposed upon the women's hockey team a ban on post season play for the 2017-18 season following an alcohol incident in March of 2017.
On May 22, 2019 the board that runs the Minnesota Intercollegiate Athletic Conference, which is made up of the school presidents, announced that St. Thomas University was being removed from the conference involuntarily effective the spring of 2021. The release cites competitive parity as the main reason for the move. The university has been dominant in league competition accounting for about half of all MIAC championships (team and individual) since 2013. No announcement was made about the university's plans for joining a new conference.
The university is working of getting a waiver from the NCAA to make the jump from division III to Division I. The university has been accepted as a member of the Summit League. The Summit League does not sponsor either football,men's ice hockey or women's ice hockey but the possibility exists that the men's program may end up in the reformed Central Collegiate Hockey Association when it starts in 2021-21. The conference has seven members and the addition on St. Thomas would make a good fit geographically and balance the league with 8 members. The women's program is a possibility for the Western Collegiate Hockey Association's women's league. The process for moving from Division III to Division I usually takes 12 years but the NCAA can grant a waiver as the school is under a unique set of circumstances with be removed from a conference for being too good to maintain a competitive balance within the conference at the D-III level and that there is only one other D-I all sports university in the state of Minnesota.