O'Connor was ordained a priest in Rome on June 1, 1833 by then-Archbishop (later Cardinal) Costantino Patrizi Naro. He was then appointed Vice-Rector of the Pontifical Irish College in the same city. He also served as an agent of the Irish bishops with the Holy See, and gained the friendship and esteem of both Pope Gregory XVI and Cardinal Nicholas Wiseman. In 1834, he returned to his native country and served as a curate in Fermoy. He was also chaplain at for the convent of the Presentation Sisters in Doneraile. He applied for the position of professor of dogmatic theology at Maynooth College but was persuaded by a colleague, Peter Kenrick, to pursue a teaching position in the United States.