Manning was born of a Low Church family and was educated at Harrow and at Balliol College, Oxford (B.A., 1830), gaining some reputation as a debater. He lacked the financial backing to enter politics like his friend William Ewart Gladstone, but worked for a year in a minor post of the colonial office and returned to Oxford as fellow of Merton College. He was ordained (1832) in the Anglican Church and was given a living in Sussex. By 1835 he had become an adherent of the Oxford movement. In 1841 he became archdeacon of Chichester.
By 1845 when William George Ward was degraded, Manning had become prominent in the Oxford movement, and his letters of succeeding years, as well as his visit to Rome (1847), foretold his following of John Henry Newman and Ward into the Roman Catholic Church. When the bishop of Exeter was compelled by the privy council (1850) to institute G. C. Gorham to a benefice despite Gorham's open disbelief in the doctrine of baptismal regeneration, Manning left the Church of England and entered (1851) the Roman communion.