He commenced studying for the priesthood, and in 1950 progressed to St Patrick's Seminary, Manly and then Propaganda College, Rome where he was ordained a priest by Archbishop Pietro Sigismondi on 7 December 1954.

[3] In 1957 Dougherty obtained his Doctorate of Divinity in spiritual theology from the Pontifical Urban University in Rome, and immediately returned to Australia and was appointed assistant priest of St. Mel's in Campsie.

[4][5] In a very unusual move by Dougherty, on the day before his retirement was announced, he issued a statement denouncing a booklet written by a priest of his diocese.

[8] Dougherty resided in Bathurst until his death at St Catherine's Aged Care facility on 30 August 2010 following a short battle with lung cancer.

During the numerous eulogies at the mass, it was reported that Dougherty was considered a "... very humble and deeply spiritual man whose witness and example were a source of inspiration for all in the diocese of Bathurst".