On July 8, 1954, Scanlan was appointed Auxiliary Bishop of Honolulu and Titular Bishop of Cenae. On September 21 of that year, Scanlan's episcopal consecration took place. On November 10, 1967, Scanlan was appointed Apostolic Administrator of Honolulu and took charge of the administration of the diocese.
On March 6, 1968, he was appointed the Bishop of the Diocese of Honolulu. On June 30, 1981, Scanlan retired but continued to be active as Bishop Emeritus. He died in California on January 31, 1997 and was buried in the crypt at the Cathedral of Our Lady of Peace alongside the remains of missionary Bishop Louis Maigret.