Stephen was educated at Geelong Church of England Grammar School and entered Trinity College, at the University of Melbourne in 1878. He was ordained in 1884 and was a curate and parish priest in Melbourne before becoming chaplain of Trinity College and then the warden of St John’s Theological College. From 1894-1899, Stephen was vicar at St Andrew's Church, Brighton and was Dean of Melbourne from 1910 until his elevation to the episcopate.
He retired to Melbourne in 1928, where he died on 7 July 1956 at Kew, aged 95. His funeral service was conducted by Archbishop Booth at St Paul's Cathedral on 9 July.
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