Hannington was born at Hurstpierpoint in Sussex, England, on 3 September 1847. A poor scholar, he left school at fifteen to work in his father's Brighton counting house. At twenty-one, Hannington decided to pursue a clerical career, and entered university at St. Mary's Hall, Oxford, where he again proved to be a desultory student. In 1872, the death of his mother spurred a change in Hannington's life: he was awarded his B.A., and on 1 March 1874 was ordained as a deacon, and took charge of the small parish of Trentishoe in Devon.