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He was the son of Walter Wilkins, a citizen and goldsmith of Oxford. He was born at Fawlsly, near Daventry, in Northamptonshire, in the house of the Reverend and well-known Mr. John Dod—who wrote on the Commandments—as he was his grandfather on his mother’s side. He was taught Latin and Greek by Edward Sylvester, a noted Grecian who kept a private school in the parish of All Saints in Oxford. His proficiency was such that at thirteen years of age he entered as a student at New-Inn, in the Easter term of 1627. He did not stay there long, but was moved to Magdalen Hall under the tuition of Mr. John Tombes, where he took his degrees in arts. He afterwards entered into Holy Orders and was first chaplain to William, Lord Say, and then to Charles, Count Palatine of the Rhine and Prince Elector of the Empire, with whom he continued for some time.
Upon the breaking out of the Civil War, he joined with the Parliament and took the Solemn League and Covenant A religious and political agreement between the Scottish Covenanters and the English Parliamentarians during the Civil War.. He was afterwards made Warden of Wadham College by the Committee of Parliament appointed for reforming the University. Having been created Bachelor of Divinity on April 12, 1648, he was put in possession of his wardenship the following day. The next year he was created Doctor of Divinity and, about that time, took the Engagement A loyalty oath to the Commonwealth of England. then enjoined by the powers in being.
In 1656, he married Robina, the widow of Peter French (formerly Canon of Christ Church) and sister to Oliver, then Lord Protector. In 1659, he was made Head of Trinity College in Cambridge by Richard, the Protector, which was the best preferment in that University.