The Briton, who was working for an international aid organisation, was killed yesterday by a gunman who followed him into his compound in the capital Juba, according to colleagues who asked not to be named.
Britain's Foreign Office confirmed that a British national had been killed.
"We can confirm the death of a British national in South Sudan. We stand ready to provide consular assistance to the family," a Foreign Office spokesman told AFP.
South Sudan's police said they had no information on the killing.
The country is awash with guns, and shots are often heard at night.
South Sudan is heavily dependent on international aid organisations for humanitarian aid, with the UN estimating that 2.5 million people are in a state of emergency or crisis, just steps short of famine.
International charities have warned of increased harassment, surveillance and threats of expulsion from the government. In August 2014, gunmen murdered at least six South Sudanese staff members of international aid agencies.
Fighting broke out in South Sudan, the world's youngest nation, in December 2013 when President Kiir accused his sacked deputy Riek Machar of attempting a coup.
No overall death toll for the war has been kept by the government, rebels or the UN, but the International Crisis Group estimates that at least 50,000 people have been killed.
