Frere was born in Cambridge, England, on 23 November 1863, the younger son of Philip Howard Frere and his wife Emily, née Gipps. His siblings were Arthur, Ellen and Lucy. Lucy became the wife of Wilfred J. Barnes. He was educated at Trinity College, Cambridge and Wells Theological College; and ordained in 1889. His first post was as a curate at Stepney Parish Church. He was Examining Chaplain to the Bishop of Southwark from 1896 to 1909.