Masudur Rahman, the deputy police commissioner, said on Sunday that the militant leader, who was identified after analyzing CCTV footage, was arrested on the outskirts of the capital, Dhaka, on Saturday.
"Acting on a tip-off, the counter-terrorism police unit arrested him," Rahman said.
The 25-year-old man, identified as Mojammel Hossain, the head of the intelligence wing of the al-Qaeda-inspired militant group Ansar Ullah Bangla Team, was suspected of taking part in the killing of writer Avijit Roy.
In the primary interrogation, he confessed to his involvement in the killing of four other secular activists.
Roy, a US citizen of Bangladeshi origin, was hacked to death by machete-wielding assailants in February 2015 while returning home with his wife from a Dhaka book fair. Roy's widow, Rafida Ahmed, was seriously injured.
The arrest came after another suspected killer of Roy was detained earlier this month.
Police say the militant group is behind the murder of more than a dozen secular bloggers and rights activists. The Bangladeshi government has been under pressure to protect the rights of writers in the country.
Bangladesh has seen a string of deadly attacks targeting bloggers, foreigners and religious minorities.
In the most serious recent attack in July 2016, gunmen stormed a cafe in the diplomatic quarter of Dhaka and killed 22 people, most of them foreigners.
Al-Qaeda and the Daesh Takfiri terrorist group have also claimed responsibility for a series of killings over the past few years.
The Dhaka government has denied the presence of such groups, blaming domestic militants instead.
But security experts say the scale and sophistication of the cafe attack suggested links to a wider network.
Police and army commandos have killed over five dozen suspected militants and detained hundreds since the cafe attack.