The victim was killed by a falling wall as he and other schoolmates tried to escape the school in Magsaysay on Mindanao island.
Local hospitals have received 10 injures after the quake.
The quake damaged homes, multi-storey buildings and classrooms in a region where hundreds are still displaced by a quake that killed at least five earlier this month.
The Philippine Institute of Volcanology and Seismology (Phivolcs) said the inland tremor hit at a depth of 7 km, about 25 km southeast of Tulunan town.
The earthquake was also felt in strongly in Kaidapawan City, Sarangani province, Davao City, Koronadal City, Cagayan de Oro City, General Santos City, Zamboanga City, and Bukidnon province.
Earlier on October 16, a 6.4- magnitude earthquake hit Mindanao.
The Philippines is regularly hit by quakes as the country is on the Pacific “Ring of Fire,” a horse-shoe shaped band of volcanoes and fault lines circling the edges of the Pacific Ocean.