[2] Bishop Thomas Grace then sent him to the College of Propaganda in Rome; Shanley made the journey with Reverend John Ireland, the future archbishop of the Archdiocese of St. Paul and Minneapolis.

[2] Shanley made it a priority to serve minorities and the destitute;[5] he conducted segregated services for African-American Catholics in the basement of the cathedral.

On November 15, 1889, Shanley was appointed the first bishop of the newly erected Diocese of Jamestown in North Dakota by Pope Leo XIII.

He received his episcopal consecration on December 27, 1889, at the Cathedral of Saint Paul, from then Archbishop Ireland, with Bishops Grace and Martin Marty serving as co-consecrators.

Shanley donated a large portion of the funds that he had personally raised for the new cathedral to reconstruct the city after the fire.

[6] In 1891, Shanley wrote the Fargo Argus defending Native Americans living on the Turtle Mountain Indian Reservation.