Suraj (6) and his sister Khusbu (4) went missing from their home in Sachendi area last evening, police said.
After a prolonged search, their bodies were found from a well situated outside the village, a senior police officer said.
"During initial investigation, it was found that both were killed before their bodies were thrown into the well," said Amitabh Yash, DIG, Kanpur.
Police are suspecting personal enmity as the reason behind the crime.