he was on her way to a floating school on the Agusan Marsh in the Philippineswhen the huge reptile capsized the boat, the provincial government said.
The girl fell into the water during the attack on Saturday, but her headless body was not discovered until two days later.
A classmate who was with her was rescued by a man who had been escorting the pair in another boat, said Ruel Hipulan, head of the private group which runs the school.
"It's a monster crocodile," he said. Witnesses said the crocodile was about 30ft (nine metres) long.
The floating school has been temporarily closed while a search for the crocodile is under way.
Around 100 members of the Manobo tribe have been forced to leave their houses, which sit on the lake on stilts, amid fears of another attack.
The Agusan Marsh in southern Mindanao island is a sanctuary for protected species including freshwater crocodiles and soft-shell turtles.
Crocodile attacks in the area are rare but the reptiles have become aggressive recently because they have had little to feed on.
The lake has been swollen for the past several months, causing fish to scatter to other places