London Fire Brigade (LFB) quickly brought the flames in a front carriage under control at the central London station.
Around 100 people were rushed out of the busy station at around 10.50am as a precaution amid false rumours that a bomb had gone off.
Two people were checked by paramedics but no-one was injured.
British Transport Police said the fire was thought to have been caused by an electrical fault and there were no suspicious circumstances.
Pictures and videos posted on social media showed flames and people fleeing the station.
Several fire engines and London Ambulance Service vehicles could be seen outside the station by Trafalgar Square, which reopened at about 1.15pm.
LFB said that only a small number of people were on the affected service to Hastings in East Sussex.
Eileen Harris, 60, and her son Daniel, 26, were on the train on platform six to travel to Tunbridge Wells in Kent when the fire started.
Ms Harris said: “Suddenly the doors burst open and a woman ran through shouting there’s a bomb on the train, everybody get off.
“We ran away towards the opposite end of the station because I thought that if there was a bomb, they’d probably take out the concourse.
“But the staff kept saying to us come back in and we really didn’t want to come back through the station, because by then there was thick smoke.
“We were marshalled out here and told that it’d be closed for a very long time, and then the emergency services turned up.
“Where the fire was there were big bangs and pops and flashes. And the smoke, the smoke was the worst thing.”
Mr Harris said: “There was fire and lots of thick smoke, so we assumed that there was a bomb ripping through the train.
“People were running through the train and my first thought was the reason they’re running down the train is because they can’t get off. No-one really knew what was going on.”
London Fire Brigade said about 5% of the front carriage was alight.