The order, signed by Gen Prayuth and announced late Thursday, gave no details except to say that the dismissal was to ensure orderly and appropriate conditions on the State Railway. The Peace and Order Council leader made the order to dismiss Mr Prapat effective immediately.
The dismissal was made amid a public outcry and social criticism that the rapist and murderer identified as Wanchai Saengkhao, 22, should be executed in order to prevent a similar incident from occurring again in future.
Critics said that a railways official should take responsibility for the incident.
The incident took place last Saturday, after victim "Nong Kaem" boarded an SRT sleeper car in Surat Thani to go back home to Bangkok with family members.
Her body was found early Tuesday morning and the suspected rapist was apprehended.
Mr Wanchai, employed the SRT as a sleeper carriage attendant, reportedly told police that he took the girl from her bed, raped her and pushed her out of the running train.
He also threw away her clothing and the sheet of her bed along the railway between Wang Pong and Khao Tao stations in Hua Hin district.
The initial autopsy at the Police General Hospital found that the victim had a wound in her head and scratches on her body.
Even after learning of his dismissal, Mr Prapat attended a Buddhist religious ceremony for "Nong Kaem", held at a temple in Bangkok’s neighbouring province of Nonthaburi.
Mr Wanchai is now being detained in Prachuap Khiri Khan province. Police objected to his temporary release on bail.