Chowdhury, who has evaded arrest for over one and a half years, was apprehended on Friday noon from Jamayetul-Ulum-Al Islamia Madrasa.
It is the same institution where an explosion left three dead, Chittagong Metropolitan Police Additional Commission SM Tanvir Arafat said.
The explosion took place at the Jamayetul-Ulum-Al Islamia Madrasa at the city's Lalkhan Bazar on Oct 7 in 2013.
The blast shattered the third floor of the hostel and left several injured. Police filed three cases over the incident under homicide, explosives and acid Acts in which nine people were accused.
That included Chowdhury, his son Mufti Harun, three other madrasa teachers and two students.
Although the madrasa authorities tried to pass it off as a laptop burst, police recovered grenades, acid and huge amount of explosives during a raid on the madrasa after the blast.
On Oct 10, two days after the explosion, a press conference on behalf of the Hifazat-e Islam central committee claimed the incident was an arranged 'drama' by police and media.
Mufti Harun was arrested at Raozan two days later but his father managed to evade arrest.
Chittagong-based radical group Hifazat’s Nayeb-e-Amir Izaharul is also the chief of Nezame Islam Party, which opposed Bangladesh’s independence in 1971.
His son Harun is also a leader of Hifazat and a teacher at the madrasa.
RAB in December 2010 arrested Mufti Izaharul over charges of involvement in militancy. He was later released on bail.