The explosion occurred at around 6am this morning at the entrance of the Narathiwat municipality fresh market on Phupha Phakdee Road.
Police said the five kiligramme bomb was built in a metal box and placed inside a helmet compartment of the motorcycle. A male teenager reportedly drove the motorcycle to park behind a pickup truck from Narathiwat Special Task Force 32.
The vehicle was installed with a jammer to cut mobile phone and radio signals used to trigger bombing in the southernmost province.
The bomb exploded five minutes after the youth left the motorcycle and walked into the market.
The explosion wounded one solder and five villagers shopping at the market.
Six motorcycles, two pickup trucks, that belonging to the government task force and another owned by a local resident were damaged by the explosion.
On Thursday, Thai National Security Council secretary general Paradorn Pattanatabutr signed an agreement to begin a "dialogue process for peace" with Hassan Taib, chief of the liaison office of the Barisan Revolusi Nasional (BRN) in Malaysia.
It was seen as a positive step, but is unlikely to immediately end the conflict because several other shadowy movements also fighting in southern Thailand have yet to agree to talks.