The person identified as Mufazzil Haque was arrested from Mokimnagar area of the district bordering Bangladesh on Tuesday night, official sources said.
The National Investigation Agency alleged that Haque was running a madrassa in Murshidabad district of West Bengal where youths were recruited for JMB and he was a close associate of Sajjid, who was arrested by the NIA in November last year.
His name had not cropped up during the interrogation of Sajjid but recently NIA arrested four people from various parts of West Bengal who gave some evidence to the probe agency against him, the sources said, adding after this he was placed under arrest.
The blast in Burdwan took place inside a house on October two last year, leaving two persons dead.
The National Investigation Agency(NIA) took over the case from West Bengal police few days after the explosion after international links started surfacing.
Investigators have found that Improvised Explosive Devices(IED) were being fabricated in the house and later smuggled to neighbouring Bangladesh.
The NIA has so far found that members of JMB terror group had established their network in different places like Murshidabad, Nadia, Malda, Birbhum, Burdwan in West Bengal and Barpetta in Assam, Sahibganj and Pakur in Jharkhand.
The NIA also claimed that senior members of JMB had established terrorist training centres and bomb making units in Beldanga and Mukim Nagar of Murshidabad, Nanur of Birbhum and Khagragarh and Simulia of Burdwan district.