The international NGO will also maintain the toilets, which will have separate male and female chambers, hand washing facilities and sanitary napkins.
Bangladesh has become a country free of open defecation, increasing the sanitation coverage to 99 percent from 34 percent at household level in the last decade.
But sanitation and hygiene remain a challenge in the institution and public domain.
WaterAid say they have tied up with Dhaka University as part of an effort to go beyond building toilets to ensure sanitation.
University treasurer Prof Md Kamal Uddin and WaterAid country representative Md Khairul Islam signed the MOU on Monday at the vice-chancellor’s office.
Vice-Chancellor Prof AAMS Arefin Siddique and WaterAid's Global Chief Executive Barbara Frost, Chair of Board of Trustees Tim Clark and Trustee member Anna Segall witnessed the signing.