Colonial era

On 20 April 1954, a group of missionaries from the United States arrived in the Baliem Valley, which was then part of Netherlands New Guinea. The missionary team traveled by light aircraft, landing on the Baliem River, specifically in Minimo village, with the primary mission of introducing Christianity to the Dani people of the Baliem Valley. The first missionary station was subsequently established in Hitigima. Over the following seven months, they constructed the first airstrip in the area. Some time later, the missionaries identified a more suitable site for an airfield. This site, located near the territory of the Mukoko people, became the location where a new airstrip was developed, which would later evolve into present-day Wamena Airport. The early airstrip was built by missionaries and local residents using basic tools and had minimal infrastructure, with a simple grass or compacted earth runway and no fencing.

In 1958, the Dutch colonial administration formally established its presence in the Baliem Valley, constructing a government post in the vicinity of the airstrip. In 1960, the Dutch authorities established regular air services to Wamena in response to the increasing number of tourists visiting the Baliem Valley. By 1961, De Kroonduif, a subsidiary of KLM operating in Netherlands New Guinea, operated four weekly flights between Hollandia (now Jayapura) and Wamena using Douglas DC-3 Dakota aircraft. Following the New York Agreement in 1963, the Dutch withdrew from New Guinea, and control of the airfield was transferred to the Indonesian government. The Jayapura–Wamena route was subsequently taken over by the Indonesian state-owned airline Merpati Nusantara Airlines.

Contemporary history

Following the Indonesian annexation of Western New Guinea, President Suharto ordered the upgrade of Wamena Airport to accommodate larger aircraft such as the C-130 Hercules as part of broader efforts to develop West Irian. The project, supported by the Indonesian Navy, Air Force, and the Army Corps of Engineers under Kodam XVII/Cenderawasih, aimed to improve regional connectivity and support economic activities, particularly the distribution of agricultural products from the Baliem Valley. The runway was extended from 1,400 meters to 1,900 meters, with completion originally planned for June 1971, but, the first C-130 Hercules successfully landed on 22 August 1970.

On 2 April 1977, management of the airport was transferred from the Ministry of Home Affairs to the Ministry of Transportation. At that time, Wamena Airport was already capable of accommodating aircraft such as the Fokker F27.

On 1 August 2000, approximately 100 members of the Papua Task Force (PTF), a pro-independence civilian militia, seized control of Wamena Airport after rumors circulated that refugees fleeing violence in the Maluku Islands would arrive there. Armed with bows, arrows, and clubs, they forced their way past security, set up their own guards, and took control of key areas of the airport. During the takeover, PTF members searched passengers and ransacked luggage, particularly those bound for Jayapura, while also preventing some travelers from departing. The disruption lasted several days until police forces regained control of the airport on 5 August 2000.

In the early morning of 26 September 2011, the terminal at Wamena Airport was destroyed by fire, which was suspected to have been caused by a short circuit. There were no casualties in the incident. The fire destroyed the terminal facilities, including the airport medical room, baggage area, and ticket counters. The losses were estimated at up to nine billion rupiah.