During a raid in port area of the city, the militant identified as Muijanur Rehman, 45, was arrested late last night, Joint Commissioner of Police (STF) Rajeev Mishra told PTI.
The HuJI militant was wanted in connection with the abduction of Khadim's owner Burman and is a co-associate of another militant Amir Reja Khan.
Some "suspicious objects" and pamphlets were found in his possession, Mishra said.
Rehman was hiding in Bangladesh for about 12 years and was believed to have sneaked into Kolkata in recent times.
The militant would be produced in court soon.