There were nearly 100 attacks on Afghan schools in the first half of the year, a six-fold rise from the same period in 2005, according to the agency.
At least 50 schools have been burned down and six pupils killed in different attacks, the report said.
"Today, schools are closing, students are staying home and the hard-won progress is at risk," said Patrick McCormick, a Unicef spokesman.
McCormick also said that in four southern provinces it is estimated that more than 100,000 children are shut out of schools because of their closure.
Unicef said it had no "concrete evidence" about who was carrying out the campaign. However many incidents have been blamed on fighters from the country's hardline former Taliban regime, which denied young girls access to education.
"Today, schools are closing, students are staying home and the hard-won progress is at risk"
Patrick McCormick, a Unicef spokesman.
Millions of Afghan children returned to school since the overthrow of the Taliban by US-led forces in 2001, including 1.5 million girls who had been discriminated against under their strict rule, Unicef said.
A report by Human Rights Watch, the New York-based human rights group, said in July that it had documented more than 200 attacks on schools and teachers since January 2005 and said that girls' schools had been particularly hard hit.
The human rights group blamed the Taliban as well as allied Islamist groups, local warlords and the country's "rapidly growing criminal networks" for this degradation.