Seven other students riding in the auto-rickshaw were injured in the incident.
The students were returning home from Sun Mission School in Morena, said Kotwali police station in-charge Yogendra Jadon.
The deceased were identified as Kuldeep (6) and driver Munna (35).
The auto-rickshaw was speeding when it overturned at a culvert near Bicholi on the outskirts of Morena town.
The injured students were admitted in the district hospital, Jadon said.