The military said a Boeing C-17 left Thursday for South Sudan.
"The flight was at the request of the Foreign and Commonwealth Office, who are coordinating the evacuation, which was prompted by security issues in the African state," the military said in a statement Thursday.
Western governments have issued travel warnings for South Sudan in response to political violence that erupted after President Salva Kiir accused his former vice president of attempting a coup.
Kiir sidelined former Vice President Riek Machar in a Cabinet reshuffling earlier this year.
The FCO updated its travel advisory for South Sudan, saying it was time to evacuate the country.
"British nationals wishing to leave South Sudan are strongly urged to do so now," it said.
A similar statement was issued Wednesday by the U.S. State Department. The U.S. Embassy in Juba said U.S. citizens should consider leaving South Sudan as soon as possible.
The independent Sudan Tribune reported South Sudanese forces have lost control of Bor, the capital of restive Jonglei state, to rebel forces.
South Sudan gained independence in 2011 under the terms of a peace deal, brokered with Washington's help, which ended the Sudanese civil war.