In 1880 he was appointed vice-rector of College of St. Francis Xavier in Antigonish, Nova Scotia, and had risen to rector by the end of his service in 1891.

He was pastor in Arichat and D'Escousse, Nova Scotia before becoming Vicar Apostolic of Western Newfoundland (St. George's) and Titular Bishop of Nilopolis in 1895.

Shortly after being appointed as Archbishop, NcNeil was charged with completing St. Augustine's Seminary and the Canadian Catholic Church Extension Society created by his predecessor Fergus Patrick McEvay.

Under McNeil, thirty more parishes were established, including those with non-English speaking immigrants in Toronto.

[1] Under his leadership, the China Mission Seminary, later renamed the Scarboro Foreign Missionary Society, and the Newman Club were established.