Patriarch Ignatius Aphrem II has spoken to the BBC as coaches have been bringing thousands of people back to the town, and the nearby city of Palmyra, after the two areas were retaken by Russian-baked Syrian forces and their allies last week.
He claimed three women were among those killed, while five more Christians are still unaccounted for, thought to be dead.
The patriarch reports nearly 300 Christians stayed in al-Qaryatain when IS took it, with some dying trying to escape while other were killed for breaking rules imposed by the militants.
Dozens of Christians were among hundreds of residents abducted when IS seized al-Qaryatain, many of whom were freed when their families paid ransoms.
Speaking to the BBC, Patriarch Ignatius Aphrem II said he remains focused on striving towards peace among different faiths.
He said: "We lived this situation for centuries, we learned how to respect each other, we learned how to live with each other," said the patriarch. "We can live together again, if we are left alone by others."
The loss of al-Qaryatain and the ancient city of Palmyra represent further blows for IS, as President Bashar al-Assad has made a number of gains in the last few months.