The duo had reportedly gathered at Matuail to plan sabotage in Dhaka city, members of the CTTC said.
The accused persons used to communicate online with the members of Neo JMB at various levels, including its top leaders.
One of the arrested persons has been identified as Sakib Ahmed Chowdhury alias Jaki, while the identity of the second accused has not been disclosed yet.
Neo-JMB is a breakaway faction of the old Jamaat-ul-Mujahideen Bangladesh (JMB), which is linked with global terror outfits such as the Islamic State. It came into focus after the terror attack at the Holey Artisan restaurant in Dhaka in July 2016 that killed 20 people.
The Investigation Division of the CTTC launched an operation in Matuail under the Jatrabari police station on Tuesday and arrested the duo, recovering two mobile phones from their possession, said Iftekhairul Islam, Additional Deputy Commissioner of the Dhaka Metropolitan Police.
The arrested militants were reportedly involved in carrying out propaganda on social media and other online platforms, inspired by violent extremist and militancy, the police said.
Sakib worked as a freelancer after completing his studies from a private university in Sylhet, while the other accused, a juvenile, was a student of Sylhet Government Primary Pilot High School, according to the CTCC.