Eastern South Dakota went through several Catholic jurisdictions before the Vatican erected the Diocese of Sioux Falls: The Catholic presence in present-day South Dakota began in 1842 when the French missionary Reverend Augustin Ravoux from the Diocese of Saint Paul traveled up the Missouri River to baptize children at Fort Pierre.

[3] On August 12, 1879 Pope Leo XIII established the Vicariate Apostolic of Dakota, with territory taken from the Diocese of Saint Paul.

In 1880, Marty persuaded Benedictine sisters from Missouri to assist him in ministering at Fort Yates, a center of the Yankton Lakota people[7] The first Catholic church in Sioux Falls, St. Michael's, was dedicated in 1881.

In 1889, Leo XIII suppressed the vicariate and erected the Diocese of Sioux Falls, which included all of the new State of South Dakota.

[10] During his 25-year tenure, O'Gorman increased the number of priests in the diocese, and erected numerous churches, schools, and hospitals.

[12][13] The Benedictine Sisters Order opened the Sacred Heart School of Nursing in Yankton in 1905, later to become Mount Marty University.

In 1922, Monsignor Bernard Mahoney, spiritual director of the Pontifical North American College in Rome, was appointed bishop of Sioux Falls by Pope Pius XI.

[21] After Mahoney died in 1939, Pope Pius XII named William O. Brady of St. Paul that same year to serve as the next bishop of Sioux Falls.

[24] Hoch fostered ecumenical relations with other faiths and helped establish the South Dakota Association of Christian Churches.

[26] During his tenure, Dudley developed several ecumenical ministries serving the poor, and fostered many retreat and spiritual renewal programs.

To replace Carlson, Pope Benedict XVI appointed Monsignor Paul J. Swain of the Diocese of Madison.

[31][32] In 1978, Reverend Bruce MacArthur, originally from the Diocese of Sioux City, was convicted in Texas of trying to rape a disabled woman in a nursing home.

[33][34] The diocese was sued in 1995 by Kurt Brick, who claimed that he was sexually abused, starting at age 14, by Reverend William Neuroth at Bishop O'Gorman High School.

[33] In 2003, Native Americans alumni of several Catholic boarding and mission schools in North and South Dakota started filing lawsuits against the Dioceses of Sioux Falls and Rapid City and several religious orders.

[37] Bishop Carlson invited the South Dakota Attorney General to inspect the diocese's files on past and present priests.