The airline was established in 1987 and was previously known as Avia. It acquired Salair on 15 July 1991 and Highland Air in March 1997. A partnership was forged with Scandinavian Airlines (SAS) which acquired a 25% stake in April 1998. The owners were Salenia (72.7%), SAS (25%) and Janus (2.3%). The operational division of Skyways was separated from the sales division in 2009. During 2010 there was some restructuring regarding ownership. SAS sold its share of the company at a loss, and eventually it was acquired by the asset management company Manswell Enterprises Limited, controlled by Ihor Kolomoyskyi. In 2011 Skyways merged with another Manswell controlled company, the Gothenburg-based airline City Airline, as Skyways. They also bought the Danish Cimber Sterling and got in mind to become Scandinavias biggest regional airline. As of December 1, 2010 the operation, sales and marketing of the airline functioned again as one unit under Avia Express continuing the use of the brand Skyways.
On 22 May 2012, Skyways Express AB and City Airline AB filed for bankruptcy; Cimber Sterling was filed for bankruptcy earlier that month.