Phelips became a Freeman of Portsmouth in April 1660 and was warden of Salcey Forest, Northamptonshire from July to August 1660. He became groom of the bedchamber to King Charles in 1661 with a salary of £500 a year. Also in 1661, he was called to the bar and was elected Member of Parliament for Stockbridge in the Cavalier Parliament. He was a commissioner for assessment for Surrey from 1661 to 1664 and for Wiltshire from 1661 to 1669, and a commissioner for loyal and indigent officers for London, Westminster and Somerset in 1662. He became involved with Samuel Sandys' fenland reclamation and was commissioner for sewers for the Bedford level from 1662 to 1663 and conservator for the Bedford level from 1663 to 1665, from 1666 to 1667 and from 1669 to 1670, In 1671 he was commissioner for encroachments at Windsor. He was elected MP for Andover in 1685. From 1685 to 1687 he was privy seal and commissioner for the great wardrobe. He was Chancellor of the Duchy of Lancaster from 25 May 1687 until 21 March 1689.
