He was educated at the Halifax grammar school and entered at Christ's College, Cambridge, 21 June 1642.
Milner was probably with Lake at Oldham in 1651; it has been inferred that he was schoolmaster at Chadderton appointed in August 1641.
At the Glorious Revolution of 1688 he joined the nonjurors, was deprived of all his preferments, and retired to St. John's College, Cambridge, where he lived in comparative ease.
His only son, Thomas, vicar of Bexhill, Sussex, proved a great benefactor to Magdalene College, Cambridge, under his will dated 5 September 1721.
Milner left in manuscript a translation in Latin of the Targum on the First and Second Book of Chronicles, and other works on Scriptural chronology and current ecclesiastical controversies.