In Tweihineh, "the Islamic State of Iraq and the Levant... Has forbidden girls in primary education and above from attending school unless they wear fully Islamic clothing including an abaya (gown), gloves and a veil," the Syrian Observatory for Human Rights said.
Citing activists in the ISIL-controlled northern village, the Britain-based Observatory also said boys were told to dress in what the extremist group considers Islamic clothing.
They must wear "traditional Pakistani clothing and a cap", said the Observatory, which relies on activists, doctors and lawyers across Syria for its information.
The main opposition National Coalition condemned ISIL's "aggression" against the churches in the city of Raqa.
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It said the jihadist group "is outside the Syrian revolution and does not at all represent the Syrian people's aspirations".
Activists in opposition-controlled areas have reported escalating abuses by ISIL against local rebels and civilians, including kidnappings and public executions.
Despite fears of retaliation, there have been anti-ISIL protests.
Today, amateur video distributed online showed activists in Raqa staging an anti-ISIL demonstration and carrying a large cross that the jihadists had torn down.
By committing abuses "and war crimes" in rebel-controlled parts of Syria, "ISIL is doing Assad's regime a great service", he added.
"For hundreds of years, people in Syria have lived side by side with each other, and we believe in freedom of religion."
Extremism is not the only obstacle to education in Syria.
The UN agency for children said this month that nearly half of Syrian children are not in school.
Of more than two million Syrians forced to flee their country, some half are children, and only a minority are in school this year.