Walter Devereux, 1st Earl of Essex, enabled him to spend some time abroad, sending information about European affairs. Having returned to England, he entered parliament in 1606 as member for Helston, and he sat in the five succeeding parliaments; in 1614 he was knighted, in 1616 he became master of requests and later surveyor of the court of wards. In 1618 his friend Buckingham procured for him the position of secretary of state. Naunton's strong Protestant opinions led him to favour more active intervention by England in the interests of Frederick V, and more vigorous application of the laws against Roman Catholics. Gondomar, the Spanish ambassador, complained to James, who censured his secretary. Consequently in 1623 Naunton resigned and was made master of the court of wards. He died at Letheringham, Suffolk, on the 27th of March 1635.
Naunton's valuable account of Queen Elizabeth's reign was still in manuscript when he died. As Fragmenta regalia, written by Sir Robert Naunton, it was printed in 1641 and again in 1642, a revised edition Fragmenta Regalia, or Observations on the late Queen Elizabeth, her Times and Favourites, being issued in 1653. It was again published in 1824, and an edition edited by Edward Arber was brought out in 1870. It has also been printed in several collections and has been translated into French and Italian. There are several manuscript copies extant, and some of Naunton's letters are in the British Museum and in other collections.
See Memoirs of Sir Robert Naunton (1814).