The bomb was hidden under rail tracks at Khok Pho district of Pattani, damaging the last carriage, Police Captain Promote Juichouy told Reuters.
The blast destroyed half the carriage and blew a big hole under the track, police said.
The three wounded people included two train workers and a female passenger. The train was heading to Bangkok.
Peace talks between Thailand’s government and Muslim separatists ended on Friday with no breakthrough but an agreement to meet again. The insurgents denied responsibility for a string of bombs last month.
A decades-old insurgency in the Muslim-majority southern provinces of Yala, Pattani and Narathiwat has claimed more than 6,500 lives since it escalated in 2004, according to the independent monitoring group Deep South Watch.
As with most such attacks, no one claimed responsibility.
The blast occurred three weeks after a series of explosions hit three of Thailand’s most popular tourist resorts and a town in the south, killing four people and wounding dozens.