In 1882, Shahan obtained a Doctor of Divinity decree and was ordained a priest for the Roman Catholic Archdiocese of Hartford in Connecticut.

[4] From 1889 to 1891, Shahan studied at the Humboldt University of Berlin (S.T.D., 1891), the Sorbonne and the Institut Catholique de Paris earning a Civil and Ecclesiastical Law licentiate's degree.

In 1891, Father Shahan was offered a position as professor of Canon and Civil Law and Patristics at the Catholic University of America, where he also taught Latin.

In addition to teaching at CUA, he was editor in chief of the Catholic University Bulletin and also lectured at nearby Trinity College.

In 1909, while Professor of Church History, he was appointed rector, when Pope Pius X declined to release Bishop John Patrick Carroll of the Diocese of Helena, Montana from his see.

Some in the academic community raised objections to the appointment based in part on Shahan's seriously impaired hearing.