The children, who have been identified as Ajay Ram and M Khan, both 10, fell in the well while playing, police post in-charge head constable Moti Singh said.
Khan's father Rasheed Khan spotted their slippers floating in the well, after which he alerted villagers as well as the police.
The bodies of the two were fished out from the well with difficulty since it was deep and sent them to the Nalkheda Government Hospital for autopsy, the police official said.