The son of a naval captain, Liddon was born on 20 August 1829 at North Stoneham, near Eastleigh, Hampshire. He was educated at King's College School, and at Christ Church, Oxford, where he graduated, taking a second class, in 1850. As vice principal of the theological college at Cuddesdon (1854–1859) he wielded considerable influence, and, on returning to Oxford as vice-principal of St Edmund Hall, became a force among the undergraduates, exercising his influence in opposition to the liberal reaction against Tractarianism, which had set in after John Henry Newman's conversion to Catholicism in 1845.