Their native Egypt has started providing chartered flights to help them leave after a video was released showing IS beheading 21 Copts.
The images were posted last month by the militant group on social media showing knives being held to the men's throats with the slogan "the humiliated followers of the Coptic Church".
Egypt immediately responded with air strikes on IS targets in Libya.
Weapons caches and training camps were bombed to "avenge the bloodshed", military commanders said.
The country also urged its citizens working in Libya to return home to escape the dangers of IS.
Christians have been fleeing across the border into Tunisia from where Egypt has been chartering planes to take them home.
It's estimated almost 15,000 Egyptians have now left Libya, according to state news agency MENA.