The front two sets of wheels on the first carriage of the 10.56 Brighton to London Victoria service came off the tracks just north of Merstham tunnel, near Redhill, Surrey.
One man was treated at East Surrey Hospital in Redhill for whiplash and some of the 105 passengers were said to be shocked.
The injured man was carried on a stretcher by firefighters up a steep embankment to a waiting ambulance.
More than 30 ambulances were on standby as emergency services launched a major incident plan but only one ambulance was needed.
The passengers were then put on double-decker buses to continue their journey to London.
Gary Butson, director of operations for Surrey Ambulance Service, said: "This incident could have been an awful lot worse.
"We launched our major incident plan involving the police, the ambulance, the fire and the health services.
"There were 10 ambulances at the site and we had 30 standing by from Kent, Sussex and London.
"Those who were not injured were put on to buses. Fortunately those buses were full."
British Transport Police were still at the scene as an investigation got under way into the incident, which happened around noon. A spokeswoman said rescue conditions were made difficult because of the muddy conditions.
The southeast of England has borne the brunt of the bad weather over the last few days, leading to localised flooding as rivers burst their banks.
"The cause of this derailment appears to be a landslide caused by the recent heavy rain," said the BTP spokeswoman.
Network Rail helped supervise the re-railing of the train which was expected to disrupt services for up to four hours as other trains were diverted around the scene.
Ian Thomson, of Surrey Fire Service, said the evacuation began at about 1.20pm and took time because of the width and height of the tunnel.