He was born at Cork, Ireland. His father was curate of the parish attached to the Protestant cathedral in Cork; his grandfather was Archbishop of Dublin. Young Magee entered Trinity College, Dublin with a scholarship at thirteen. He was ordained to the curacy of St Thomas's, Dublin, but, being threatened with tuberculosis, went after two years to Málaga, Spain. On his return he took a curacy at Bath, England and was soon appointed to the Octagon Chapel, where his fame both as preacher and platform speaker continued to spread. Some years afterwards he was made prebendary of Wells Cathedral. In 1860, poor health caused him to accept the living of Enniskillen, Ireland. In 1864 he was made Dean of Cork and chaplain to the Lord Lieutenant. Here he showed those great gifts which ultimately raised him to high office; a powerful grasp of mental, moral and political problems, combined with eloquence of a high order, illuminated with brilliant flashes of wit.
In 1868 the question of the disestablishment of the Irish Church came to the fore, and Magee threw himself into its defence with his usual energy and vivacity. The success of his orations caused Prime Minister Benjamin Disraeli to offer him the bishopric of Peterborough, England. He justified his appointment by his magnificent speech when the Disestablishment Bill reached the House of Lords in 1869, and then plunged into diocesan and general work in England. He preached three remarkable sermons on Christian Evidence in Norwich Cathedral in 1871. He took up the temperance question, and declared in the House of Lords that he would rather see "England free than England compulsorily sober," a statement which was misquoted and attacked. He was also a supporter of the movement for abolishing the recitation of the Athanasian Creed in the public services of the Church of England, believing, as he said, that the "presence" of the damnatory clauses, "as they stand and where they stand, is a real peril to the Church and to Christianity itself," and that those clauses "are no essential part" of the creed. The project was laid aside because of the hostility of a large body of the clergy, reinforced by the threat of Edward Pusey and Canon Liddon to abandon their offices if it were carried.
Magee took a prominent part in the Ritual controversy, opposing what he conceived to be romanizing excess in ritual, as well as the endeavour of the opposite party to "put down Ritualism," as Disraeli expressed it, by the operation of the civil law. His incisive way of putting things earned for him the title of the "Militant Bishop," but his efforts were ever for peace. He was not elevated to the see of York until his energies were exhausted, and died about four months after his appointment.
Magee's manifold activities, his capability as an administrator, his sound judgment, and his remarkable, insight into the ecclesiastical problems of his time, rank him among the most distinguished of English prelates.