He was born in Cork on 29 June 1840, as the fifth of five children of John Wheeler Dowden and Alicia Bennett. His famous brother was the poet, professor and literary critic Edward Dowden. Although his father was Presbyterian, John followed his mother by becoming an Anglican, although he attended both churches in his youth. When he was sixteen he became a student at Queen's College, Cork as a medical student. John began encountering health problems, problems which made it difficult to pursue his original career. In 1858, while contemplating a religious career, he enrolled at Trinity College, Dublin. He graduated in 1864 and was ordained as a deacon, moving to Sligo. In the same year he married, wedding a woman named Louisa Jones, by whom he would eventually father six children. John was ordained as a priest in 1865, and moved through a variety of positions slowly rising in prestige. John continued his studies and received a Bachelor of Divinity (BD) degree from Trinity College.