More than 2,000 schools were shut, while hundreds had been attacked, looted or set ablaze, Unicef said.
Boko Haram’s six-year insurgency has devastated north-eastern Nigeria, and has spread to Cameroon, Chad and Niger.
Nigeria’s President Muhammadu Buhari gave the military a deadline of the end of the month to defeat the group.
But it is likely to be extended as Boko Haram is still bombing areas despite losing towns under its control in March, says the BBC’s Bashir Sa’ad Abdullahi in the capital, Abuja.
The insurgency is said to have killed some 17,000 people and left more than two million people homeless.
Our correspondent says many schools in north-eastern Nigeria have turned into camps for those who have been forced from their homes.
Boko Haram has also targeted many schools because of its opposition to Western education, which it believes corrupts the values of Muslims.
In April 2014, it abducted more than 200 girls from a boarding school in north-eastern Chibok town, an incident which drew international attention to the insurgency.