Last month a total of 6,134 schools were shut, a 44 percent increase since May, the Norwegian Refugee Council (NRC) said.
"Over a million children in Burkina Faso are currently affected by school closures," it said in a statement, adding that these youngsters were "often traumatized by displacement and conflict."
"Only about a quarter of the children driven out of school have been given new classrooms," said the charity's country director, Hassane Hamadou.
"The majority are left without access to education, robbing them of their childhood and of their chance to become independent adults and citizens."
He urged the authorities and humanitarian groups to "urgently renew their efforts to stop this educational hemorrhage."
The UN children's agency UNICEF representative, Sandra Lattouf, warned that a child who was not in school faced a greater risk of being exploited, becoming a victim of violence and trafficking or being lured into joining an armed group.
NRC said Burkina is home to almost half of the closed schools in central and west Africa.
The worst-affected regions are Boucle du Mouhoun, East and Sahel, which are regular targets of jihadist attacks.
School closures in the country have also affected more than 31,000 teachers, 6,300 of whom have been redeployed to other schools, NRC said.
One of the world's poorest nations, Burkina Faso is battling an insurgency that spilled over from neighboring Mali in 2015.
More than 10,000 civilians, troops and police have been killed, according to one NGO estimate, and at least two million people have been displaced.
Jihadists effectively control about 40 percent of the country. Anger within the military at failures to roll back the offensive led to two coups last year.
Violence Closed Burkina Schools: NGO
OUAGADOUGOU - Nearly one in every four schools in Burkina Faso has had to close because of "rampant insecurity and violence," a Norwegian NGO said Tuesday, amid increasing jihadist attacks.