O'Flaherty was born in Carraroe, Ireland. He received his early education in Ireland and continued his studies at Lyons, France where he became fluent in French and at Montreal, Canada. He was ordained at Sioux Falls on September 15, 1901 and spent the next nine years at Chamberlain and Kimball during which time he was responsible for the construction of seven church buildings including Columbus College at Chamberlain. In 1910 he was appointed to take charge of the Holy Family Church at Mitchell where he was instrumental in the development of Notre Dame Academy in Mitchell, South Dakota.
He joined the American Expeditionary Force and was sent to France during World War I and served as a chaplain with the 28th Infantry, 1st Infantry Division. He was killed in action by shellfire on October 3, 1918. He was posthumously awarded the Distinguished Service Cross, the citation of which read: For extraordinary heroism near Very, France, Chaplin O'Flaherty displayed conspicuous gallantry in administering to the wounded under terrific fire, exposing himself at all times to reach their sides, and give them aid. In the performance of this work, he was killed.
- Origin of the Surname O'Flaherty, Anthony Matthews, Dublin, 1968, p. 40.