The girl was travelling in an overnight train Sunday from the southern province of Surat Thani to Bangkok, the Bangkok Post reported.
According to officials, the girl's naked body was found Tuesday around 4.00 a.m in Wang Pong sub-district.
Earlier Monday, a 22-year-old bedsheet replacement employee of the State Railway of Thailand, confessed to raping and killing the girl, before throwing her body out of a window.
The accused said that he he opened a window of the non-air-conditioned car where the girl was sleeping so that the wind blocked other noise before attacking her.
After raping the girl, he killed her and threw her body off the train as it was approaching the Wang Pong station.
He then threw the girl's clothes and blood stained sheets.