In addition to the native inhabitants, the district was settled relatively early by foreigners, first Chinese merchants, then the Portuguese after the fall of Ayutthaya to the Burmese in 1769. In addition to the Chinese and Portuguese, there were also Muslimsand Mon, from Burma, as well as French priests, particularly in the neighbourhood called Kudi Chin. The area still retains many Chinese shrines, mosques, and Santa Cruz Church, the second Catholic church to be built in Thailand.
The district used to be called Amphoe Ratchakhrue (ราชคฤห์) due to a nearby wat of the same name. It was renamed Amphoe Bang Yi Ruea on 11 July 1916 (after the location of the new amphoe office), and finally to Thon Buri on 17 April 1939. The district then belonged to Thon Buri Province. In December 1971 the province was merged with Bangkok to form the present day Bangkok metropolitan area.