The carrier will fly to Corfu, Crete and Santorini from 1 May. Corfu flights will be “up to one daily”, with Heraklion up to five times a week and Santorini twice weekly.
Aegean, which is based in Athens, will also station aircraft in Corfu and Santorini next summer.
Dimitris Gerogiannis, the airline’s chief executive, said: “We are now standing at the most difficult turning point of the pandemic.
“We do, however, need to plan, to adapt to the new needs of our passengers, and to create the necessary conditions for recovery as soon as health conditions allow it.
“To this end, we are announcing a major flight schedule for 2021 directly to the regions and the islands, starting next May and June.”