The Congregation of Sisters of St. Agnes founded the college in response to a Wisconsin Department of Instruction decision that nuns were not allowed to teach in public schools while wearing their religious habits.

Although Marian was founded as a women's college, the male superintendent of Fond du Lac schools attended art and music classes with his wife in 1940.

Marian had 86 full-time and 145 part-time students in 1950 who attended classes in a convent next to St. Agnes Hospital.

Increasing enrollment caused the college to move to its current 100 acres (40 ha) campus on Fond du Lac's east side in the mid-1960s.

[3] In 2021, the college was sanctioned by the American Association of University Professors "for infringement of governance standards".

Marian University offers the BA, BS, and MA degrees, as well as a variety of licensures and certificates.

The Campus Ministry at Marian University provides many activities for students to deepen their understanding of the Catholic tradition: weekly Mass, retreats, sacraments, Scripture study, Rosary, adoration of the Blessed Sacrament, and outreach to the local area.

Students participate in sports at the NCAA Division III level in women's basketball, golf, hockey, soccer, softball, tennis, and volleyball, and men's baseball, basketball, golf, hockey, soccer, men's volleyball, tennis, and lacrosse.