The body was located 400 feet downstream from where the boy was last seen at Ten Mile Creek - near Sequoia and Kings Canyon National Park.
Fresno County search and rescue crews focused their search on an area where they found the boy's shoes on Saturday.
Dozens of search and rescue teams from the sheriff's office looked through the area with the help of a helicopter over the weekend.
Park officials shut down the water flow from nearby Hume Lake which gave them a break in their search.
Authorities say the boy was visiting the area with his family from New Jersey.