In October 1868 Corrigan became vicar-general of Newark, a diocese then including all the state of New Jersey.
In 1880 Bishop Corrigan was made coadjutor, with the right of succession, to Cardinal McCloskey, archbishop of New York, under the title of archbishop of Petra; and thereafter nearly all the practical work of the archdiocese fell to his hands.
On the death of Cardinal McCloskey in 1885 Archbishop Corrigan became metropolitan of the diocese of New York.
The earlier years of his archiepiscopate were disturbed by his controversy with Edward McGlynn (1839-1900), a New York priest (and a fellow-student with Corrigan at Rome), who disapproved of parochial schools, refused to go to Rome for examination, and was excommunicated in July 1887, but returned to the church five years later.
Archbishop Corrigan became his coadjutor in 1880 because of the failure of McCloskey's always delicate health.