The airport first opened in March 1939. At that time, this was merely a piece of flat agricultural land. The first aeroplane (a Junkers Ju 52) carried the initial passengers to the site. During the Second World War, the airfield was the site of the Battle of Heraklion during the Battle of Crete, in 1941. Civilian operations ceased; but in the autumn of 1946, traffic resumed, introducing the DC-3 aircraft. At first, the airport only offered very basic service, with only primitive installations on the site in the form of three tents, smoke for wind determination, and storm lamps for runway lighting. In 1947, the first (small) terminal was erected. Hellenic Airlines started commercial flights in 1948. At that time, a total of 4,000 people were served. The year 1953 saw the construction of a paved runway which was initially 1,850 meters long and oriented as 09/27. The next major event followed in 1954, when a four-engined DC-4 aircraft landed for the first time at the airport. In that year, the airport handled approximately 18,000 passengers. From 1957 onward, the new Olympic Airways used the airport, starting services with the DC-6 aircraft. From 1968 until 1971, the runway was extended to 2,680 m (8,790 ft) and a new terminal and other facilities were constructed, essentially making it a new airport. On 18 March 1971, the first charter flight from abroad operated to the airport. The new airport itself was officially inaugurated on 5 May 1972. In 2025, farmers protesting against the delayed payment of European Union subsidies occupied the airport's apron, resulting in disruptions to aviation. The airport is scheduled to cease operations in 2027 and to be replaced by the (expanded and renamed) Kasteli Airport.