Stanley was Dean of Westminster, one of five children of the Right Reverend Edward Stanley, Bishop of Norwich. He was educated at Rugby and Balliol College Oxford. Between 1856 & 1864 he was Regius Professor of Ecclesiastical History and Canon of Christ Church, Oxford. In 1864 he became Dean of Westminster, a post which he held until his death in 1881.

In 1852 Stanley travelled to Egypt and Palestine, and produced a best-selling account of his observations, Sinai and Palestine in Connection with Their History, which is still being reprinted.