The deceased, identified as Sandeep, was left unnoticed in the basement of the house in Radhakishanpura area, an official at the Sikar district collector office said.
A rescue team evacuated him after breaking the door and rushed him to a hospital, but he died on the way.
Sikar has so far recorded 15 cm of rainfall. Parts of the city's low-lying areas were facing flood-like situation, the official said.
The downpour caused water-logging in areas including Bajaj Road, Nawalgarh Road and Radhakishanpura, he said.