A Star Alliance member since June 2010, it operates scheduled and charter services from Athens and Thessaloniki to other major Greek, European and Middle Eastern destinations.

Aegean's first commercial flights were in May 1999 from Athens to Heraklion, Crete and Thessaloniki with two new wholly owned British Aerospace Avro RJ100.

In February 2010, initial shareholder discussions took place to consider co-operation between Aegean Airlines and Olympic Air fueling rumours of a possible merger.

[23] The intent was for the merged carrier to be a Star Alliance member, despite the fact that Olympic Air was forging ties with SkyTeam pre-merger.

[27] Star Alliance welcomed the proposed merger, releasing a statement stating "The integration teams from both sides will soon meet to assess the necessary steps, in order to guarantee a smooth transition of the merged Aegean Airlines and Olympic Air operations into the Star Alliance network".

[30] Additionally, commissioner Joaquin Almunia stated that the merger would have led to higher prices and lower quality of service for Greeks and tourists traveling between Athens and the islands.

[29] On 21 October 2012 Aegean Airlines announced that it had struck a deal to acquire Olympic Air, pending approval by the European Commission.

[41] At the end of December 2020, the European Commission approved a €120 million state aid, to compensate for the financial losses due to the COVID-19 pandemic.

[43] In February 2022, Aegean announced the installation of Wi-Fi equipment to the entire A320neo family fleet as well as select older A320ceo aircraft.

[44] By April 2024, the original A320neo family order was extended from 30 to 50 aircraft, four of which will be A321LR models in with a dedicated long-haul cabin with "lie-flat" business class seats.

Losses were incurred 2010–2012, amidst the economic crisis for Greek tourism and the economy in general; passengers carried fell to 6.1 million, although the load factor increased to 74.3%.

The charter flights connect popular holiday destinations in Greece to Italy, France, United Kingdom, Poland, Israel, Romania, Sweden, Denmark, Estonia, Finland, Norway, Slovenia, Austria, Germany, Hungary, Ukraine and other countries.

[87] By March 2014, passenger cabins across the entire fleet were retrofitted with brand-new reclining Aviointeriors Columbus Two seats, which are thinner and lighter, allowing the addition of an extra row.

During the A320neo delivery presentation, Aegean Airlines unveiled the new logo and livery inspired by Greek sky and seas, historical architecture and the country's design heritage.

It is a rebranding of Miles&Bonus, the former frequent flyer program of Aegean as well as a replacement for Olympic Air's Travelair Club.

[citation needed] Gold members of Miles+Bonus, or those with Gold status in another Star Alliance airline, as well as passengers traveling on business class on an Aegean Airlines or other Star Alliance flight, all have access to the three Aegean Business Lounges in Athens, Thessaloniki and Larnaca.