Militant Sifat, who also goes by the aliases Shamim and Moinul Islam, was arrested early on Wednesday in Gazipur's Tongi on the outskirts of Dhaka, said police.
The Detective Branch produced Sifat, who is believed to be one of the masterminds of the October 2015 murder, before a Dhaka court and sought ten days in custody to interrogate him.
Metropolitan Magistrate Ahsan Habib granted six days.
Sifat had a Tk 200,000 bounty on his head.
He is one of the six militants for whom police had announced a total bounty of Tk 1.8 million three months ago for information leading to their arrest.
Police believe the six were involved in the murder of bloggers, secular writers and Dipan.
Prior to Dipan’s murder, Ahmedur Rashid Tutul, owner of Suddhaswar, another publishing house, and secular writers Tarek Rahim and Ranadipam Basu came under vicious attack at Tutul's office at Lalmatia on the same day.
The three, however, survived the attack with critical injuries.
Both Tutul and Dipan had published books by the secular writer-blogger Avijit Roy, who was killed in a similar fashion in February last year.
Dipan was the only son of the writer and Dhaka University teacher Abul Kasem Fazlul Haque.
Before and after Avijit's murder, several other bloggers, writers and secular platform Ganajagaran Mancha activists were brutally murdered by suspected militants in the past several years.
In a media briefing on Wednesday, police's counterterrorism unit chief Monirul Islam said Sifat was present at the scene with five others when Dipan was murdered.
During initial interrogation, Sifat said dismissed Bangladesh Army Major Syed Md Ziaul Haque masterminded the deadly aasault, according to Monirul, an additional police commissioner.