[2] Shea graduated from St. John's College (now Fordham University), and entered the Society of Jesus in 1844;[3] during this time he added his middle name of Gilmary ("servant of Mary").

His comprehensive study of early Indian missions in America, the Discovery and Exploration of the Mississippi Valley with the original narratives of Marquette, Allouez, Membré, Hennepin and Anastase Douay, was published later that year.

Shea turned his attention to literature, and was connected in an editorial capacity with Frank Leslie's publishing house, and later edited the Catholic News, but for many years his attention was given to historical research in preparation of his History of the Catholic Church in the United States (1886–92), the fourth volume of which was in process of publication at the time of his death in Elizabeth, New Jersey.

[3] In 1879, Shea wrote in The American Catholic Quarterly Review that Italians and Chinese should not be permitted to immigrate to the United States.

He praised Irish Catholic immigrants as "in the main pure, virtuous, healthy in body and mind, industrious, anxious for work" whose faults were due only to alcohol abuse, resulting in brawling.

[8] However, Italian immigrants, in Shea's view, largely "belonged to the dangerous class in their own country" and were part of a "steady criminal emigration".