"Approximately 6.9 million girls and boys, one in three school-aged children, do not go to school in Sudan," the UN children's agency UNICEF and aid group Save the Children said in a joint statement.
"A further 12 million will have their school years heavily interrupted by a lack of sufficient teachers, infrastructure, and an enabling learning environment to make them reach their full potential."
Children in impoverished Sudan have for years faced difficulties with access to education, especially those living in rural areas.
Monday's statement said access to education has been impeded by the exacerbating socio-economic situation, recurring conflicts and school closures during the Covid-19 pandemic.
"Once children drop out of school, the chances of girls and boys returning to school are low," it said, noting that girls are especially vulnerable.
Sudan, one of the world's poorest countries, has been grappling with unrest that deepened following last year'smilitary takeover led by army chief Abdel Fattah al-Burhan, triggering cuts to crucial international aid.
The military takeover derailed a fragile transition put in place following the 2019 ouster of president Omar al-Bashir, whose three decades of rule were marked by economic hardship, government mismanagement and internal conflict.
Unrest after last October's military takeover sparked near-weekly protests, fed into a spiralling economic crisis, and saw a rise in ethnic clashes nationwide.
Hundreds of teachers in Sudan have also staged protests in recent months over low wages.
"No country can afford to have one-third of its school-age children with no basic literacy, numeracy, or digital skills. Education is not just a right, it's also a lifeline," said Mandeep O'Brien, UNICEF representative in Sudan.
In June, the UN said a record 15 million people in Sudan, around one-third of the population , were facing "acute food insecurity" and warned that the situation was likely to get worse.