In c.1633, Sterne became chaplain to Archbishop Laud. From 1642 he held the rectories of Yeovilton and Harleton. A Royalist, he was arrested and imprisoned by the Parliamentarians later the same year. In 1644 he was formally dismissed as Master of Jesus and in 1645 he lost his rectories, although he was released from prison.
At the Restoration in 1660, Sterne was appointed Bishop of Carlisle, from where he was translated to York in 1664. He is said to have been one of those who assisted in revising the Book of Common Prayer in 1662. He also assisted Brian Walton with the English Polyglot Bible and himself wrote Summa Logicae (published posthumously in 1685). He founded scholarships at both Corpus Christi and Jesus Colleges.