The airport was established by the council in 1928. It was requisitioned by the Royal Australian Air Force during World War II for the purposes of an airbase for anti-submarine patrols. No. 71 Squadron and 'C' Flight No. 73 Squadron operated from the base from 1943 until being disbanded in late 1944. No. 12 Operational Base Unit maintained and serviced the airfield during its operation. A number of bunkers associated with the RAAF's occupation exist near the airfield, including one which has been repurposed as a gallery containing a large collection of cartoon art.

With the introduction of Fokker F28 regional jets by Airlines of New South Wales in 1983, Coffs Harbour was identified by the federal government as one of six regional centres in the state to receive airport upgrades to support their operation. These works were estimated to cost $9.6 million, involving the construction of a new runway, taxiways, apron and terminal building, and an air traffic control tower, all expected to be completed by September 1985. Projections at this time were that the airport would handle in excess of 26,000 aircraft movements and 112,000 passengers by the year 2000.

In 1993 Air New Zealand operated a promotional flight from Auckland using a Boeing 737, with the support of the Coffs Harbour Council. Despite hopes that such charters would help to drive tourism in the region, the flight was reported to have run at a loss of close to $60,000.

In August 1999 the runway was widened from 30 to 45 metres to accommodate Boeing 767s.

From the early 2000s, the airport became a regular destination for training flights by cadets from the Singapore Flying College, owing to its favourable weather, surrounding high terrain and air traffic control facilities.

In 2015, Coffs Harbour Airport secured funding from the Government of New South Wales to expand the apron space to allow more parking for narrowbody jet aircraft, as well as upgrades to the security screening and baggage facilities. These works increased the number of parking bays at the terminal from three to five, which can be occupied simultaneously.

In late 2020, the City of Coffs Harbour entered into a 50-year agreement, leasing the airport to Palisade Investment Partners to operate and develop the airport. This agreement included the development of the 23 ha (57 acres) Airport Enterprise Park, adjacent to the general aviation facilities north of the main terminal. This construction resulted in the permanent closure of taxiway E5, which was equipped with edge lighting to facilitate the movement of aircraft to the general aviation area at night. During construction, the smaller runway 10/28 was also closed, fueling speculation that it too would be permanently closed and converted to a taxiway. While this was denied by the airport's management, it was conceded that the future of the runway was under review, with safety given priority over development.