He was with her at Kenninghall when young Edward VI died and Lady Jane Grey ascended the throne for nine days.
He was named Master of the Henchmen and a member of the Privy Council, and Mary's husband Philip II of Spain gave him a pension.
Being a devout Catholic and supporter of Mary, she had him retained, through personal letters, in Parliament and granted him the stewardship and keepership of the manor of Beaulieu alias Newhall at Boreham, Essex,[4] and a house in London on Canon Row in Westminster.
Wharton was a Member (MP) of the Parliament of England for Cumberland 1542, 1545, 1547 and October 1553; for Hedon April 1554, Yorkshire November 1554; Northumberland 1555 and 1558.
Wharton died on 14 June 1572 at his house on Canon Row, and was buried in Westminster Abbey.