The British man, whose name has not been released, was brought by ambulance to the Boeing C-17 cargo plane. The flight took off at around 1250 GMT.
The UK department of health said in a statement the man was not seriously ill and it had decided to repatriate the British national following clinical advice.
Upon arrival at the RAF Northolt airbase in Britain, he will be transported to an isolation unit at the Royal Free Hospital in London, the department said.
"Protective measures will be strictly maintained to minimize the risk of transmission to staff transporting the patient to the UK and healthcare workers treating the individual," said Paul Cosford, director for health protection at public health England.
The outbreak of the hemorrhagic fever in West Africa — the worst since the disease was discovered in the jungles of Central Africa in 1976 — has so far killed at least 1,427 people, mostly in Sierra Leone, Liberia and neighbouring Guinea. Five deaths have also been reported in Nigeria.
Two American doctors who contracted Ebola in Liberia and were evacuated to the United States left hospital last week after receiving treatment with an experimental drug, ZMapp.
The US-based manufacturer, Mapp Biopharmaceutical, has said limited supplies of the drug have already been exhausted.
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