Ruthall had a long series of ecclesiastical preferments. In 1495 he had the rectory of Bocking, Essex (whose priest is called the Dean of Bocking), in 1502 he became a prebendary of Wells, and in 1503 Archdeacon of Gloucester, Dean of Salisbury and chancellor of Cambridge. In 1505 he was made prebendary of Lincoln; Henry VII, who had already made him a privy councillor, appointed him Bishop of Durham in 1509, but Henry died before Ruthall was consecrated. Henry VIII confirmed his appointment, and continued him in the office of secretary. He was part of the skeleton council that accompanied Henry VIII to the Tower of London at the beginning of his reign, following the death of Henry VII. In 1510, with Richard Foxe and Thomas Howard, Earl of Surrey, he negotiated a fragile peace with France.