Bernard graduates with a BA in mathematics from Trinity College Dublin in 1880, is elected a Fellow there in 1884, and is later a member of the council of the university, where he holds the office of King’s Lecturer of Divinity from 1888 to 1902.
Bernard is appointed treasurer of St. Patrick’s Cathedral, Dublin, by the Dean Henry Jellett in 1897. On Jellett´s death, in December 1901, Bernard becomes a favorite to succeed him as Dean, a position to which he is elected by the chapter of the cathedral on February 6, 1902. He serves as such until 1911, when he is appointed Bishop of Ossory, Ferns and Leighlin. In 1915 he is appointed Church of Ireland Archbishop of Dublin, serving until 1919.
A prolific scholar, in many fields, including Church history, theology and philosophy, Bernard is the president of the Royal Irish Academy from 1916 to 1921 and Provost of Trinity College Dublin from 1919 to 1927. He is a member of the Board of National Education in Ireland, in which capacity he serves as examiner of mathematics in the 1880s. He is regarded as an unrepentant Unionist, representing their interests as a delegate to the 1917–18 Irish Convention.
Bernard marries his cousin Maude Nannie Bernard in 1885. They have two sons and two daughters. In April 1915 his son, Lieutenant Robert Bernard of the 1st Battalion of the Royal Dublin Fusiliers, is killed in action during the Gallipoli campaign. He is commemorated at V Beach Cemetery by the Commonwealth War Graves Commission.
John Bernard dies in Dublin on August 29, 1927.