The incident took place in New Usmanpur area in the morning.
Hari Om, who hails from Gujarat, had come to his in-laws' house to take back his wife who had left him after marital discord.
The wife, however, refused to return to Gujarat which enraged Hari Om, who then allegedly threw his son from the third floor of the residential building.
The child was rushed to Guru Teg Bahadur Hospital where doctors declared him brought dead.
Police said the man has been arrested.