At the request of John Baptist Miège, Vicar Apostolic of Leavenworth, two Benedictine monks arrived in Atchison from Doniphan and opened St. Benedict's College, a boarding school, in 1858.

The monks, who had recently arrived in the Kansas Territory, then moved their community to Atchison and founded the present-day St. Benedict's Abbey.

It expanded to include commerce subjects to cater to the needs of the local population, which was primarily pioneers and settlers.

In 1924, Mount St. Scholastica's Junior College was opened so these young women could continue their tertiary education.

[16] The following year, the college added a nursing program dedicated to Mother Teresa of Calcutta who once visited Mount St. Scholastica in Atchison.

[18] The college's Discovery Program gives students the opportunity to create and present original projects in any discipline.

In that time, most faculty members and academic departments have taken an active role in sponsoring student projects.

Other active religious groups on campus include Communion and Liberation, Pax Christi, Ravens Respect Life, Partners in Prayer (in conjunction with Mount St. Scholastica), Great Adventure Bible Timeline, Fellowship of Christian Athletes, Households and Varsity Catholic.

[20] Campus worship opportunities[21] including Life of Prayer, adoration of the Blessed Sacrament, traditional Catholic processions and Guadalupe Day.

A daily rosary was added at the campus grotto to commemorate the 100th anniversary of the Marian apparitions at Fatima.

[20] Students are invited to pray the Divine Office with the monks in St. Benedict's Abbey or the sisters of Mount St. Scholastica Monastery.

Retreats, conferences, and performances that college ministry offers to students includes "Jam for the Lamb,” and BC Koinonia.

[20] The school built Mary's Grotto, located in the center of campus, and Archbishop Joseph Naumann dedicated it in 2009.

Men's sports include baseball, basketball, cross country, football, lacrosse, soccer, track & field (indoor and outdoor), and wrestling; women's sports include basketball, cross country, lacrosse, soccer, softball, track & field (indoor and outdoor), and volleyball; and co-ed sports include cheerleading, dance, and spirit squad.