In 1768 he transferred as colonel to the 15th Regiment of Foot and retired to Yorkshire, where he succeeded his father in 1771 to the baronetcy and his estate near Beverley. He took the additional name of Thompson on inheriting the Thompson estates in Yorkshire from his wife's family in 1772 (reverting to Hotham in 1787) and commissioned Thomas Atkinson of York to rebuild Dalton Hall between 1771 and 1775.[2] He was knighted KB in 1772.
Promoted Major-General in 1772, he retired from the Army in 1775, was gazetted full general (as Sir Charles Thompson, Bt) in 1793 [3] and died at Dalton Hall in 1794. He had married Lady Dorothy Hobart, the daughter of John Hobart, 1st Earl of Buckinghamshire, and had one daughter. He was succeeded as baronet by his brother Sir John Hotham, 9th Baronet.