1999	The Flight Safety Foundation and the Hellenic Civil Aviation Authority both name the company as a business with excellent organization which has achieved exceptionally high safety standards.
2000	The European Regions Airline Association (ERA) awards Aegean Airlines its Bronze Award Airline of the year 2000/01.
2000	The company is singled out for distinction by British Aerospace.
10/2002-6/2003	JAR OPS1 certification process for the whole operational sector of Aegean, with the support of Lufthansa Consulting. Flight staff receives special JAR OPS training at the Lufthansa training centre.
2004	ERA Gold Award. Aegean Airlines receives the Gold Award Airline of the year 2004/05.
2005	For the third time Aegean Airlines receives an award from the ERA - the Silver Award Airline of the year 2005/06.
2005	3 awards for Aegean Airlines from Athens International Airport: As the fastest-growing airline in the western European market For the highest percentage increase in passenger traffic in the domestic market, and As the fastest-growing company overall using Athens International Airport, for 2004
2006	The company receives a fourth award from the ERA - the Silver Award Airline of the Year 2006/07.
2006	A Gold Medal for Aegean from Athens International Airport. The award was made for the highest increase in passenger numbers in 2005, and the highest percentage increase in passenger traffic in the domestic market.
2006	Aegean receives IOSA certification. Successful completion of the inspections conducted as part of the IOSA programme (IATA Operational Safety Audit) in June 2005.
2007	Aegean receives award from Athens International Airport as the company with the largest increase in passengers at the Eleftherios Venizelos Airport in 2006, and for the highest percentage increase in passenger numbers in the domestic market.
2007	Aegean wins the ERA's Palme d'Or award. The Palme d'Or is an award for sustained performance and excellence and is given to companies which have been named ERA Airline of the Year three years in succession.
2008	ERA Gold Award. Aegean receives the Gold Award Airline of the year 2008/09 at the prestigious European Regions Airline Association, Airline of the Year awards ceremony at the 2008 General Assembly.
2009	Aegean named top Regional Airline in Europe by SKYTRAX