AEGEAN is strengthening its routes as of 2025, it will offer two new destinations from Athens and seven new direct domestic flights from regional bases. According to a company announcement, from the beginning of the new year, AEGEAN will connect Athens to Iraq with direct flights from Athens Airport to Erbil International Airport. The flights will start on February 23 and will operate twice a week, every Wednesday and Sunday. On April 14, 2025, the airline's direct flights from Athens to Azerbaijan will also resume, operating every Monday and Friday with Airbus 320neo aircraft. 

On the domestic network, AEGEAN is adding four new direct routes from Heraklion to Rhodes, Naxos, Corfu, and Kos. From the island of Rhodes, two more new direct flights to Chania and Santorini will be operated from June 2025. More specifically, flights from Heraklion "Nikos Kazantzakis" airport to Rhodes "Diagoras" airport will be operated daily. The first flight is scheduled for March 2025. From June, routes from Heraklion to Kos (with three weekly flights), Naxos, and Corfu, with two weekly flights, respectively. Flights connecting Rhodes with Chania will be operated by ATR 42-600 aircraft twice a week. It is already planned to increase them to four in the middle of the tourist season. Flights from Rhodes to Santorini will be operated three times a week, every Tuesday, Thursday, and Saturday. From June 2025, AEGEAN will also connect Thessaloniki directly to the island of Syros, with three weekly flights every Tuesday, Thursday, and Saturday.