Scanlan arrived in 1873 to find about ninety Catholics in Salt Lake City and Ogden combined. Traveling by horseback, stagecoach, or rail, he visited miners and railroad workers in camps and junctions throughout the territory. Over the next decade, he opened churches for them, schools for their children, and hospitals for their sick, first in Salt Lake and Ogden, then in Silver Reef, Frisco, Park City, and Eureka. Archbishop Joseph S. Alemany named Scanlan vicar forane in 1879.
Assisted now by other priests and the Sisters of the Holy Cross from Notre Dame, Indiana, he established parishes in Provo, Bingham, and Tooele. Holy Cross Hospital, All Hallows College, Kearns-St. Ann's Orphanage, and Judge Mercy Home and hospital rose up in Salt Lake City.
The Holy See in Rome created the Vicariate of Utah and Eastern Nevada on 23 November 1886 and consecrated Scanlan bishop on 29 June 1887 at St. Mary's Cathedral in San Francisco. He cared for 5,000 souls in an area of 154,000 square miles, the largest geographic entity in the American Catholic Church. The vicariate became the Diocese of Salt Lake on 27 January 1891.
Scanlan's crowning achievement was the construction of the Cathedral of St. Mary Magdalene, dedicated in Salt Lake City 15 August 1909. Rather than triumphant, however, he felt exhausted, anxious about what still remained to be done. He died in 1915 and lies buried within his cathedral, an enduring symbol of pioneer faith.