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Police said Idris Ahmed, 42, was arrested for the alleged rape of about 12 boys aged between 12 and 19 at a madrassa in Dhaka's Dakshin Khan neighbourhood.
One offence was committed just a week before his arrest and Ahmed filmed the assault, said a police statement Monday.
Ahmed is the third teacher from an Islamic seminary to be arrested on rape charges this month after the detention of two head teachers accused of raping female pupils.
A number of former male madrassa students have in recent weeks said on social media that they had been raped or sexually molested by teachers and older students.
The mainstream media has remained mostly silent on the issue, largely due to the sensitivity of the subject in the conservative nation.
But the country was shocked this year by the murder of 19-year-old Nusrat Jahan Rafi, who was burned to death on the alleged orders of a madrassa headteacher after she refused to withdraw a sex assault charge against him.
Rights groups have expressed alarm about the growing number of sex crimes on children.
The Manusher Jonno Foundation, a rights group, published a report saying 399 children, including eight boys, had been reported as victims of rape and attempted rape in the first six months of the year.
Sixteen victims had died, it added.
Abdus Shahid, head of the Bangladesh Shishu Adhikar Forum, another children's rights group, said there was "a culture of impunity" surrounding the violence.
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