Kanhaiya Lal raped his 10-year-old niece on the night of July 25 and strangulated her before throwing the body into a nearby well, police commissioner Biju George Joseph said.
The girl, who had gone to attend a birthday function on that night, went missing and her body was recovered next day, he said.
Later, during interrogation, Lal confessed to his crime, the top cop said, adding that a case has been registered against him.