The church was designed by an unknown architect with Carpenter Gothic, Eastlake, and Shingle Style influences and constructed in 1888 with funding from Saint Katharine Drexel. Drexel, a wealthy heiress turned nun, led missionary efforts in Native American and African American communities. According to the congregation, the history of the mission symbolizes an “uneasy alliance” and “cultural clash” between 19th-century Native American communities and Christian missionaries. Through education, the U.S. government intended for English to replace native languages. Yet, while missionaries at St. Francis Xavier taught school in English, they preached in the Crow language. By 1891, Jesuit missionaries had baptized about half of the reservation’s Crow population.

Today, 95 percent of the congregation is Native American. St. Francis Xavier, now governed by the Capuchin order, recognizes its uneasy past and works to actively celebrate Crow culture. St. Labre Catholic Indian Schools run a prekindergarten through 8th grade school out of the church, serving 140 Crow children, and the church runs feeding programs and provides backpack meals for students. Crow language and culture are critical parts of the curriculum. The school has improved the quality of education and served as a major source of employment in the area.

A National Fund grant of $100,000 with $328,824 in matching funds raised by the congregation supported restoration of the building’s exterior. This project included rebuilding the roof, repair and repainting of windows, and replacement of trim detail. The current pastor attests to the project’s impact, “There has been an outpouring of gratitude and awe for how this Mother church of the Crow Reservation continues to speak to the faithful 138 years after it was completed.”