Wharton was the eldest son of Thomas Wharton, 1st Baron Wharton, by his first wife, Eleanor, the daughter of Sir Brian Stapleton of Wighill, Yorkshire. After his mother"s death his father married, on 18 November 1561, Anne Talbot, widow of John Bray, 2nd Baron Bray, and daughter of Francis Talbot, 5th Earl of Shrewsbury.
He was with her at Kenninghall when young Edward VI died and Lady Jane Grey ascended the throne for nine days. Sir Tom escorted Mary to Framlingham Castle and, upon her accession, to the Tower of London. He served as High Sheriff of Cumberland for 1547 and as Member of Parliament for Cumberland in 1544-1545, 1547, and 1553, for Hedon, Yorkshire in 1554, for Northumberland in 1555, and again for that county as well as for Yorkshire in the parliament of 1557-1558.
Being a devout Catholic and supporter of Mary, she had him retained, through personal letters, in Parliament and granted him the Manor of Newhall in Boreham, Essex and a house in London on Canon Row in Westminster.
When Mary died and Elizabeth became queen, Thomas was excluded from Parliament and retired to Newhall. Seven years later he inherited the title of Baron which he held for four years.
Wharton was a Member (Member of Parliament) of the Parliament of England for Cumberland 1542, 1545, 1547 and October 1553. Foreign 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.
He was named Master of the Henchmen and a member of the Privy Council.
