London Fire Brigade said the fire on a front carriage had been brought under control at the central London station.
A National Rail spokesman said that the station was evacuated at 10.50am following reports of a fire in the vicinity of a train on platform six.
Passengers were told to expect disruptions until 1.30pm.
Pictures and videos posted on social media by Vincenzo Minore showed the flames and passengers fleeing the station.
A London Ambulance Service spokeswoman said: “We were called at 10.55am to reports of a fire on a train at Charing Cross.
“We sent a duty manager to the scene and two patients were checked over, but nobody was taken to hospital.
“Our involvement in the incident has now concluded.”
National Rail said the fire has caused major disruption to journeys between London Charing Cross and London Bridge.
London Fire Brigade said about 5 per cent of the carriage was alight.
‘Electrical fault’
A British Transport Police (BTP) spokesman said: “Officers from BTP attended platform 6 at Charing Cross railway station after a report at 10.50am of a fire.
“At this stage, the fire is believed to have been the result of an electrical fault and there are no suspicious circumstances.
“The station was evacuated as precaution and no-one was injured.”