Thomas Wharton was born on 13 Mar 1758, the son of Thomas Wharton of Lauriston, Edinburgh who was Commissioner of Excise in Scotland. His mother was Judith Massey. Young Thomas sailed to India on 9 Feb 1777 and was initially a lieutenant in the 35th Sepoy Battalion from July 1787. In Dec 1788 he transferred to the 1st Native Cavalry. But he was appointed Adjutant of the 36th Sepoy Battalion from 31 Oct 1791 to 1794. He served in the 2nd Rohilla War, at the battle of Bitaurah. He was then a lieutenant in the 2nd Native Cavalry and promoted to captain on 14 Feb 1796, in which rank he was 2nd in Command to his brother-in-law. He was promoted to major on 1 Nov 1798 and transferred to the 3rd Native Cavalry. On 29 May 1800 he raised and commanded the 5th Native Cavalry at Ghazipur with the rank of lieutenant-colonel. His command did not last long as he drowned while crossing the Kali Nadi, 2 miles east of Serai Miran, United Provinces. He died on 21 Jan 1802, drowned along with his horse and his dog.
He was married to Sarah Paulina Skardon on 12 Aug 1789, at Cawnpore. They had a son, Thomas Ramsay Wharton who briefly served as a cavalry officer and became a Surveyor in the Opium Department. Sarah died in 1838.