STORY: A viral video showed the toddler's neighbors rescuing him from a river of mud.
The child is now recovering in the San Juan Lurigancho hospital, Peru's state news agency said.
More video, released by the Joint Command of the Armed Forces of Peru, showed rescuers helping children and their parents cross torrents of muddy waters running through the street so they could attend school in the town of Chosica.
The heavy rains have left over 3,000 people homeless in the Lima region, government authorities said.
At least six people have died in Peru over the last few days as a powerful cyclone unleashed torrential rains, battering hundreds of homes and causing major disruptions in northern parts of the country.