The severely damaged tracks have been repaired, said Aekkarat Sriarayanpong, the agency’s public relations director, as quoted by The Nation, a leading Thai newspaper.
"Officials have already finished checks to ensure safe operations," he said.
Two round trips are scheduled every day on the route.
The train was travelling from Songkhla's Hat Yai District in Thailand to Padang Besar in Malaysia when a bomb blast derailed it on December 3, leaving the train tracks severely damaged. Fortunately, no one was injured in the blast.
A subsequent blast on December 6 killed three engineers and wounded four others, prompting a temporary suspension of the service while the tracks were being repaired.
Police speculated that insurgents were behind the blasts and that their goal was to deter tourism and damage economic growth.
With the journey taking just one hour and tickets costing only 50 baht ($1.46), the shuttle train is a cheap way to travel between the two countries. The route is regularly used by tourists in Thailand who travel to Malaysia on "visa runs."