Polonia Airport was the site of several accidents. It is located in the centre of the city, giving a challenging takeoff path and a relatively short runway. The development of Kualanamu Airport initiated in 1991. In a visit to Medan, Azwar Anas, Minister of Transport at the time, stated that for the sake of aviation safety, a new airport would be developed outside of the city of Medan.

Preparation of construction began in 1997, but the Asian Financial Crisis that started in the same year postponed the development of it. Demands for the new airport continued following the Mandala Airlines Flight 091 accident in September 2005 that occurred shortly after taking off from Polonia for Jakarta. This accident killed the incumbent North Sumatran governor at that time Tengku Rizal Nurdin and his predecessor Raja Inal Siregar, who died a day later. This accident also involved ground casualties with at least 50 casualties, as the airport is very close to overcrowded residential areas and the runway was only 3,000 metres (9,843 ft), which although considered long for European standards, is short for Indonesian standards due to it being at a lower latitude from the equator, meaning it is warmer and as a result the air is thinner, which ultimately means that longer runway distances are needed.

All 1,365 hectares (3,370 acres) of land was acquired between 1995 and 1997 and with the certificate Exploitation Rights (Hak Pengelolaaan) No. 1 on 29 November 1999 and 100% of the land belonged to PT Angkasa Pura II. Between 1999 and 2006, some people used parts of the land illegally as agricultural land and PT Angkasa Pura II (AP II) offered them monetary compensation to move elsewhere. Construction resumed on 29 June 2006, shortly before the first anniversary of the crash of Mandala Airlines Flight 091. Jusuf Kalla, vice President of Indonesia at the time, laid the first cornerstone. This marked the construction of Kualanamu after several years with no progress. Computer renderings showing a T-shape design were posted on the company's website. A visualization of the airport is also released. It was then predicted that the airport would be completed by 2010. With land acquisition as the biggest hurdle for this project, the airport's opening was delayed until 2013 due to lack of local government awareness. On 22 July, a trailer for the airport was released.

Soft opening

A soft opening to the public was done on 25 July 2013. The airport's first commercial departure was a domestic Garuda Indonesia GA181 ferry flight from Soekarno–Hatta International Airport Terminal 3 touching down at approximately 05:00 WIB.

Grand opening

The airport was officially opened by President of the Republic of Indonesia Susilo Bambang Yudhoyono, which was marked by the signing of the stone inscription plaque on 27 March 2014.