Construction and opening

Matahora Airport was constructed to provide Wakatobi Regency with safer and more reliable air transportation. Before the airport was built, Wakatobi could only be reached by sea, where waves reaching up to 7 metres frequently disrupted travel, limiting mobility and hindering the development of tourism. This led the then-Regent of Wakatobi, Hugua, to push for the construction of a new airport to serve Wakatobi.

The airport was also built so that it can serve as a potential major backup airport for Haluoleo Airport in Kendari and other airports in eastern Indonesia. Given its strategic location, Matahora Airport was considered to have the potential to serve as a transit and diversion airport for the region. In the event of adverse weather conditions preventing aircraft from landing at Haluoleo Airport or airports in Maluku, Matahora Airport could serve as an alternative diversion airport, alongside Sultan Hasanuddin International Airport in Makassar and I Gusti Ngurah Rai International Airport in Denpasar, Bali.

Construction began in 2007, with an initial 1,400-metre runway, with an investment of 100 billion Rupiah from the Southeast Sulawesi provincial government. The airport was inaugurated on 22 May 2009 by then-Minister of Transportation Jusman Syafii Djamal, coinciding with the inaugural Susi Air flight between Wakatobi and Kendari. In the same year, Express Air inaugurated the Jakarta–Makassar–Wakatobi–Baubau route, operating Boeing 737 Classic aircraft on the Jakarta–Makassar leg and Dornier 328 aircraft on the Makassar–Wakatobi–Baubau sector.

Contemporary history

Initially, the airport was managed by the Wakatobi Regency Government before being transferred to the Directorate General of Civil Aviation (DGCA) of the Ministry of Transportation in 2015. Matahora Airport is currently managed by the Matahora Airport Administration Unit (UPBU Matahora), which operates under the DGCA. The airport has played an important role in reducing Wakatobi's geographic isolation while supporting the growth of tourism and the local economy. The number of visitors increased from approximately 3,000 in 2009 to 17,000 in 2015, contributing to Wakatobi's designation as one of Indonesia's national priority tourism destinations and part of the government's "New Bali" initiative.

In November 2015, Matahora Airport received the "Best Airport Award 2015" from Majalah Bandara, an Indonesian aviation publication.

Between 2013 and 2015, the airport underwent major renovations and expansions, including the extension of the runway and apron to accommodate more and larger aircraft, the construction of a new terminal, and improvements to other airport facilities. The overall project cost approximately Rp80 billion.

Several airlines have operated at the airport over the years, including Susi Air, Express Air, Merpati Nusantara Airlines, Wings Air, and Garuda Indonesia. Following the temporary suspension of flights during the COVID-19 pandemic in 2020, government subsidies enabled Wings Air to resume services in 2022–2023. In October 2024, Super Air Jet became the first commercial narrow-body airline to serve the airport, operating Airbus A320 flights between Makassar and Wakatobi. However, the airline only operated for about one month, allegedly due to the lack of government subsidies to support the continuation of the route. Wings Air again suspended its Kendari–Wakatobi route in May 2025. Currently, FlyJaya is the sole airline operating the Kendari–Wakatobi route.

IIn July 2026, TransNusa inaugurated a new Wakatobi–Denpasar route, providing a direct air link between two of Indonesia's major tourist destinations.