The citizens, who had registered with the Egyptian embassy in Tripoli requesting to return home, were flown back on an EgyptAir flight.
The evacuation comes amid escalating tensions between rival armed groups in the city.
The ministry said the move followed directives from President Abdel Fattah El-Sisi to monitor the welfare of Egyptians in Libya, ensure their safety, and assist those wishing to return.
Clashes erupted in Tripoli on 12 May, raising fears of further escalation.
The Egyptian foreign ministry has set up an operations room to track developments, support citizens on the ground, and respond to their needs.
Libya remains divided between a United Nations-recognized government in Tripoli and a rival administration in the east.
Despite periods of relative calm since the 2011 uprising, violence continues to flare between competing armed factions.
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