Nusrat Jahan Rafi, 19, was doused with kerosene and set on fire on the roof of her Islamic school on 6 April, days after filing a complaint.
Headmaster Siraj Ud Doula, targeted in the complaint, is among those charged.
Police say he ordered her murder from prison when she refused to withdraw her accusations against him.
They described the preparations for the killing as being like a "military plan".
The case sparked mass protests in Bangladesh and shone a spotlight on the vulnerability of victims of sexual assault and harassment in the country.