 With his reputation secured, Farquhar ran a very successful business until his retirement in 1813 with health problems.Farquhar died in London in March 1819 and was buried at St Martin-in-the-Fields in Westminster.His baronetcy passed to his eldest son, Sir Thomas Harvie Farquhar, 2nd Baronet, although it was his second son Robert Townsend Farquhar who was most successful, becoming the governor of Penang and Mauritius and subsequently a Member of Parliament.