In 1940–1941, the Soviet Union, which was occupying Estonia at the time, established a military airfield on the site of the present-day Air Base. After the war, Ämari served as a reserve airfield and, in 1952, was converted into a main airfield. In the 1970s and 1980s, it was primarily home to Su-24 naval aviation attack aircraft and transport aircraft.
The Republic of Estonia took over Ämari Airfield in 1994. Two years later, the airfield was placed under the administration of the Ministry of Defence. The Air Base as an Estonian Air Force unit was established on 15 May 1997.
Until 2004, it was possible to complete conscript service in the Military Police Squadron of Ämari Air Base. The squadron’s task was to ensure the security and defence of the base. Today, the Air Base is staffed only by active-duty regular service members and civilian employees.