A spokesperson for the military said government forces entered the village of Let Yet Kone to clear rebel "terrorists" and accused the Kachin Independence Army, a rebel group, and the People's Defence Force (PDF), an umbrella organization of armed guerrillas, of using children as "human shields."
The military said it had brought two injured children by helicopter to the hospital.
CNN could not independently verify details of the incident.
According to reports in the Mizzima and Irrawaddy news portals, army helicopters had opened fire on the school housed in a Buddhist monastery in the village.
Some children were killed on the spot by the shooting, while others died after troops entered the village, the reports said.
Two residents, who declined to be identified due to security worries, said by telephone the bodies were later transported by the military to a township 11 km (7 miles) away and buried.
Images posted on social media showed what appeared to be damage including bullet holes and blood stains at a school building.
In a statement on Monday, UNICEF, the UN Children's Fund, offered its condolences to the parents and families who lost children during the raid. "Schools must be safe. Children must never be attacked," the group said.
In a statement after Friday's violence, the NUG accused the junta of "targeted attacks" on schools and called for the release of 20 students and teachers it said had been arrested following the air strikes.
Documented violent attacks on schools surged to about 190 in 2021 in Myanmar from 10 the year before, according to Save the Children, a non-governmental organization.
Use of schools as bases by both the military and armed groups also increased across the country, the organization said in a report this month, disrupting education and endangering children.
"The junta's barbarity and callous disregard for human life aims to chill the anti-coup protest movement," Human Rights Watch's Pearson said earlier this year.
"European Union member states, the United States, and other governments should show the junta that there will be a reckoning for its crimes."