Huizhou Pingtan Airport was first built in February 1953 as Huiyang Pingtan Airport and covered an area of 5,225 mu (畝). It was a second‑class Air Force wartime airfield constructed for national defense. For decades, it served as an important military base and played a key role in air‑defense operations along China's southeastern coast during the 1960s and 1970s. From 1985 to 2002, Huizhou Airport operated civil–military joint flights. During this period, more than a dozen air routes were opened, with over 12,000 aircraft movements and more than one million arriving and departing passengers. These services played a significant role in promoting Huizhou's economic and social development.

In 2002, civil aviation operations were suspended following national policy adjustments that required the military to withdraw from commercial activities.

The airport's reconstruction and expansion project was relaunched in March 2011, when the Guangdong Airport Authority and the Huizhou Municipal Government signed the Framework Agreement on Jointly Promoting the Operation and Development of Huizhou Military–Civil Airport (共同推进惠州军民合用机场运营与发展合作框架协议). On 8 April 2014, the National Development and Reform Commission and the General Staff Department of the PLA jointly approved the feasibility study report for the airport's reconstruction and expansion. Construction began on 25 June 2014. Subsequently, the airport's airfield area passed major milestones including completion acceptance, calibration flights, test flights, and industry inspections. The terminal area also successfully passed both completion acceptance and industry acceptance, paving the way for the resumption of civil aviation operations. The airport was reopened on 5 February 2015.

To meet the rapidly growing demand for passenger throughput and to further enhance Huizhou Airport's operational capacity, the Guangdong Airport Authority launched a major expansion project in 2018. The project included the construction of a new Terminal 2 (T2) building with a floor area of approximately 16,300 m2, the expansion of aircraft stands (bringing the total to eight C‑class stands) and the relocation and reconstruction of the cargo terminal (about 1,800 m2). In June 2018, construction began on the airfield and cargo terminal components of the expansion project, both of which were completed and put into use in November of the same year. In October 2018, work commenced on the T2 terminal building and its supporting facilities. The project passed industry acceptance on 27 August 2019, and Terminal 2 officially entered service on 28 August 2019.