The explosion took place around 5.30pm at the Ban Nikhom Khok Pho station, said Pol Col Pramot Juichuay, a duty-officer at the Khok Pho police station.
Pol Capt Pramot said the bomb was placed on the tracks and exploded when the train passed over it as it passed the station.
The force of the explosion blew away half of the last carriage and killed Chawalit Khongpan, a railway employee who was sitting in the carriage at the time.
Amnuay Mapae, 49, the train station chief, was injured and was taken to Khok Pho Hospital, according to the INN News Agency. Also injured were Ekkabolloh Bilkodem, 47, a defence volunteer on the train, and Ms Supit Suwanmanee, 54, a train service employee. Their conditions were not known.
The train was on its way from the southern border town of Sungai Kolok to Hat Yai in Songkhla at the time of the blast.
Police believe the blast was linked to the southern insurgency that has claimed 6,500 lives and injured thousands more over the past 12 years.