[3] After attending La Salle Academy, Hayes studied at Manhattan College, where he excelled at philosophy and the classics and obtained a Bachelor of Arts degree with high honors in 1888.

[3] Hayes, following Farley's elevation to the episcopacy, served as his private secretary from 1895 to 1903, thereafter he was appointed chancellor of the Archdiocese and Rector of the Cathedral College.

[5] He received his episcopal consecration on the following October 28 from Cardinal Farley, with Bishops Henry Gabriels and Thomas Cusack serving as co-consecrators, at St. Patrick's Cathedral.

[5] Serving as head of the American military ordinariate during World War I, he recruited hundreds of priests as commissioned officers or chaplains.

It was speculated that the Pope delayed his elevation to the Sacred College of Cardinals because a group affiliated with New York's St. Patrick's Cathedral had stoned the Union Club for flying a British flag,[clarification needed] but Pius nevertheless warmly greeted Hayes at the consistory as "dear little brother".

[12] During the Spanish Civil War, Hayes was outspoken in his support for the fascist-nationalist forces of General Franco, "claiming that 'Loyalists are controlled by radicals and communists'."

[13][14] Hayes had a summer house in the Catskill Mountains, near St. Joseph's camp, maintained by the Amityville Dominican nuns; he once encountered a group of Klansmen there.