The airline was established on 23 October 1968 and started operations on 1 July 1971. It originally was owned by the Newcastle-based Hilder family, however in 1980 the airline was sold to Masling Airlines, a company associated with the now-defunct Ansett Australia. It operated services for Ansett Australia and later became a wholly owned subsidiary.

Aeropelican's main route was historically between Sydney and Belmont Airport in Newcastle's southern suburbs, with high frequency service using de Havilland Canada DHC-6 Twin Otters. Aeropelican originally owned this airport.

Following the collapse of parent company Ansett Australia in September 2001, Aeropelican was placed into administration. It was acquired by International Air Parts in April 2002. On 20 June 2003 the airline entered into a commercial agreement with Regional Express Airlines.

Aeropelican commenced services from Sydney to Newcastle's other airport (Williamtown, to the north of the city) on 1 March 2004. An Embraer Bandeirante started services from Williamtown on 20 September 2004 to augment the two Twin Otters used before. In March 2005 the airline discontinued service from Belmont Airport. A Fairchild Metro 23 aircraft was also added to the fleet in 2005 and the Twin Otters were withdrawn. In 2006, three BAe Jetstream 32s were ordered, with plans to announce new services. In December 2006, Aeropelican was awarded the Sydney to Inverell route licence after the previous operator Big Sky Express ceased operations. After the first two Jetstream 32s were placed into service in 2007, the Metro was withdrawn from service. In December 2007 Aeropelican announced that, subject to regulatory approval, it would commence operations between Newcastle and Tamworth, New South Wales on 12 February 2008. The airline subsequently received regulatory approval from the Civil Aviation Safety Authority and commenced operations on the route, however the following September it ceased flights to Tamworth, citing poor passenger numbers on the route.

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