The 17-year-old was last seen alive on Friday. Surveillance footage shows her entering a building in Pattaya with the suspect.
The man was later seen leaving the building alone with a large suitcase. Surveillance footage shows him loading the suitcase onto a motorcycle and driving towards an area outside the city, police said.
He was arrested early Saturday at a Bangkok airport where he was due to fly to Australia and was charged with rape of a minor.
The suitcase containing the girl's body was found shortly afterwards. The charge was expanded to include murder, which in Thailand can carry the death penalty.
The man denies the allegations.
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