O'Neill was born in Tralibane, near Bantry, County Cork. At an early age he heard the music of local musicians, among them Peter Hagarty, Cormac Murphy and Timothy Dowling. At the age of 16, he became a cabin boy on an English merchant vessel. On one of his voyages, he met Anna Rogers, whom he married in Bloomington, Illinois. The O'Neills moved to Chicago, and in 1873 O'Neill became a Chicago policeman. He rose through the ranks quickly, eventually serving as the Chief of Police from 1901 to 1905. During this time he recruited many traditional Irish musicians into the police force, including Patrick O'Mahony, James O'Neill, Bernard Delaney, Patsy Touhey, John McFadden and, James Earley. He also collected tunes from a wide variety of sources.
O'Neill retired from the police force in 1905. After that, he devoted much of his energy to publishing the music he had collected, and edited several important volumes of musical scores, including: