Lakehead Grammar School has been shut down on Tuesday on charges of harbouring militancy and inspiring extremism.
Magistrate Ilias Mehedi, who led the drive to close down the school's branches at Dhanmondi and Gulshan, said the institution's administration agreed not to run operations from Wednesday.
He said it would be a punishable offence if the school continued operations, according to a report on bdnews24.com.
The education ministry on Monday ordered the Dhaka district administration to close down the school.
Dhaka Additional Deputy Commissioner Sharif Rayhan Kabir said the administration tasked Mehedi with shutting down the school after getting the order.
Police helped the magistrate during the drive, said Gulshan Police Station OC Abu Bakr and Dhanmondi Police Station OC Md Parvez Islam.
In the order addressing the deputy commissioner of Dhaka on Monday, the education ministry also alleged the school with branches in Dhanmondi and Gulshan had no government permission.
The school was also conducting activities against the nation and its independence, according to the ministry.
An official at the education ministry said the government investigated some directors and teachers of the school after receiving complaints over their connection with militancy.
The investigators found the allegations true, the official said, requesting anonymity as he was not authorised to talk to the media over the issue.
"Some people involved with the school have been detained by the police," the official said.