The shells hit the Harabesh primary school for girls in a government-held part of Deir ez-Zor - a city currently divided between ISIS and Syrian government forces.
The Syrian Observatory for Human Rights (SOHR) reported nine female students were killed and around 20 injured when the mortar shells hit several parts of the school.
The Observatory said ISIS was responsible. It added the number of dead was likely to rise and said dozens of people had been killed and wounded in months in heavy shelling of Deir ez-Zor.
Last week Syria media said mortar attacks targeting residential neighborhoods of Damascus had killed three and wounded at least 30 people, most of them students.
It comes just a day after reports emerged of rocket and mortar fire into several Government-controlled areas of Syria, killing six civilians.
According to SANA state news agency “Jaish al Islam ” this morning fired a mortar round into the residential district of Barzeh located at north Damascus, killing one civilian and wounding nine people.'
Terrorists battling Syrian Army often shell the capital from the suburb of Eastern Ghouta.
SANA also said that in second city Aleppo in the north, 'rockets fired by terrorists hit a residential district, killing three girls and wounding another two'. The Observatory said the three dead were 'sisters aged between 16 and 19'.
The Observatory also said several people were wounded by rocket fire on the government-controlled Aleppo neighbourhood of Hamdaniyeh.
More than 250,000 people have been killed in Syria since the conflict broke out nearly five years ago, and millions more have been displaced.