In a report on the impact of conflict on education in six countries and territories across the region, the United Nation's children fund UNICEF said more than 8,850 schools were no longer usable due to violence.
It detailed cases of students and teachers coming under direct fire, classrooms used as makeshift bomb shelters and children having to cross active front lines just to take their exams.
"The destructive impact of conflict is being felt by children right across the region," said Peter Salama, regional director for UNICEF in the Middle East and North Africa.
"It's not just the physical damage being done to schools, but the despair felt by a generation of schoolchildren who see their hopes and futures shattered."
Last year alone, UNICEF documented 214 attacks on schools in Syria, Iraq, Libya, the Palestinian territories, Sudan and Yemen.
In Syria, it said education was paying a "massive price" after four year and a half years of conflict.
One in four schools have been closed since the conflict erupted, causing more than two million children to drop out and putting close to half a million in danger of losing their schooling.
In addition, more than 52,000 teachers have left their posts, saddling the country's crumbling education system with an acute skills shortage.
"Even those Syrian teachers who have ended up as refugees in other countries have faced obstacles which prevent them from working," the report said.
- 'School no longer safe' -
UNICEF said one of the worst direct attacks on a school in the region came in Yemen, where 13 staff and four children were killed in an assault on a teachers' office in the western city of Amran.
"The killing, abduction and arbitrary arrest of students, teachers and education personnel have become commonplace" in the region, the report said.
Hundreds of schools and colleges have been closed since March, when a Saudi-led coalition launched air strikes on Iran-backed Huthi rebels who had seized the capital Sanaa and several parts of the country.
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According to residents, at least seven schools in Yemen have been requisitioned by warring forces to be used as makeshift barracks or shelters for displaced families.
"The Huthis have turned some schools into barracks, depriving students of the second semester of the school year," a Sanaa-based teacher, who gave his name as Abdel Hakim, told AFP.
Abdel Rab Hassan, a director of a school in the capital, said that "tanks and anti-aircraft guns have been stationed in schools" since fighting broke out in March.
In the embattled Gaza Strip, which saw a 50-day war last year between Hamas militants and Israel kill about 2,200 Palestinians and 73 on the Israeli side, the UN said at least 281 schools had been damaged, and eight "completely destroyed".
"My children were injured in a school. They saw people injured with missing hands or legs, with wounded faces and eyes," the report quoted Gaza mother-of-two Niveen as saying.
"They no longer see school as a safe place."
- 'Generation in the balance' -
UNICEF said that violence in Iraq, where pro-government forces are battling the Islamic State jihadist group, has had a severe impact on the schooling of at least 950,000 children.
It detailed scenes among the 1,200 schools in Iraqi host communities that have been turned into shelters for those displaced by violence, with up to nine families per classroom forced to prepare meals in courtyards.
Conflict has also affected child learning in Libya -- still reeling from the 2011 ouster of longtime dictator Moamer Kadhafi -- with more than half of those displaced in the chaos reporting that their children cannot attend classes.
In the second city of Benghazi alone, the UN said just 65 of 239 schools are still functioning.
In Sudan, the agency said high numbers of internally displaced families fleeing violence in Darfur and South Kordofan states was putting untenable strain on the country's creaking school infrastructure.
UNICEF called for better informal education services in countries affected by school closures and for donor nations to prioritise education funding throughout the Middle East.
"With more than 13 million children already driven from classrooms by conflict, it is no exaggeration to say that the education prospects of a generation of children are in the balance," it said.