Nusrat Jahan Rafi had filed a police complaint against headmaster Siraj Ud Doula in late March and he was arrested.
On April 6, she attended the seminary in her hometown Feni, a small town 160 km away from Dhaka, to sit in her final examinations. she was lured to the rooftop of the building, where her attackers wearing burqas asked her to withdraw the sexual harassment complaint against Doula.
When she refused, she was doused with kerosene and set on fire.
The case sparked mass protests and underlined the vulnerability of victims of sexual assault and harassment in Bangladesh.
Prime Minister Sheikh Hasina pledged that every person involved in the killing would be brought to justice.
The police said the headmaster ordered the girl's murder from prison. They described the preparations for the killing as being like a "military plan", the BBC reported.
The attackers had planned to make it look like a suicide, the police said. But the girl, who suffered 80 per cent burns, was able to give a statement before she died on April 10.
The police in Feni formally laid murder charges on Wednesday against the 16 accused. They included students at the madrasa and two local politic from the ruling Awami League who were in prominent positions at the school.
Investigators called for death penalty for all suspects. The police said the headmaster confessed in court that he ordered the murder. Twelve others too confessed to the crime.
The two politic didn't admit involvement.
( With inputs from IANS )