Joseph Milner (1744–1797) was an English evangelical divine.
He was born at Leeds and educated at Leeds Grammar School and Catharine Hall, Cambridge. On graduation he went to Thorp Arch, West Yorkshire as assistant in a school kept by Christopher Atkinson, the vicar of the parish, received holy orders, and became Atkinson's curate. At Thorp Arch he made a lifelong friendship with the son of the vicar, Miles Atkinson, who subsequently became a leader of the evangelical party and vicar of St. Paul's, Leeds.
Still in deacon's orders Milner left Thorp Arch to become head-master of Hull Grammar School. There his pupils included William Dealtry,Samuel Marsden,George Pryme,Thomas Perronet Thompson, and Peter William Watson.
Milner was in 1768 elected afternoon lecturer at Holy Trinity Church, Hull. in that town. He now paid for the education of his brother Isaac Milner. In 1770 he became a follower of the rising evangelical school, suspected of Methodism, and the nature of his congregation at the High Church changed. He also undertook the charge of North Ferriby. Hull became a centre of evangelicalism.
Milner's chief friends were the Rev. James Stillingfleet of Hotham, and the Rev. William Richardson of York, who both shared his own religious views. In 1792 he had a severe attack of fever; in 1797 the mayor and corporation offered him the living of Holy Trinity, mainly through the efforts of William Wilberforce, but Milner fell ill and died shortly (15 November 1797). He was buried in Holy Trinity Church, and a monument to his memory was erected in it.