Catering to a large number of day-scholars, MU runs a fleet of over 50 buses for the convenience of its students and faculty. Students are charged a subsidized transportation fee for this facility. The buses cover several routes in Aligarh, Agra, Mathura, Hathras, Etah and Sasni. Students from farther-off locations typically tend to stay in the hostel. For campus residents, the University runs weekly buses to the nearby cities of Aligarh and Mathura. People availing of this facility enjoy a day out on town, with a comfortable ride back to campus in the evening.

MU places a high premium on the safety, hygiene and punctuality of its transport system. The University takes great pains to ensure these key factors, and has appointed a dedicated Transportation Department to monitor the performance of the service. In addition, MU has a fleet of cars and vans for backup transport. When some students are required to stay back late for trainings, workshops, extracurricular activities or organizational activities, the University ensures that their transportation is taken care of by this fleet.