The history of the Pardubice airport dates back to 1995 and 1994, respectively. Until that year it was a military airport and was used exclusively for military purposes. Until 1989, due to political and military reasons, civil air traffic at the airport was impossible. After that date, the change of the political conditions in the Czech Republic brought about the change in position of the Ministry of Defense concerning the possibility of opening the airport for civil operators, both domestic and foreign ones.

In 1993, several private subjects founded East Bohemian Airport a.s. company (further as EBA) with the aim of opening the airport for civil air traffic. In 1994 EBA had a feasibility study processed and started negotiating with the representatives of the Ministry of Defense. These negotiations resulted in initially sporadic flights of civil airplanes at the airport that in these times had first to be authorized by the Air Base Command. In 1995 the Ministry of Defense issued permission for EBA a.s. to utilize the airport for civil purposes.

In the same year, the Czech Aviation Authority confered on EBA a.s. the confession to operate the airport; the Ministry of Transport of the Czech Republic, Civil Aviation Department granted to EBA a.s. its assent to render handling services at the Pardubice airport. Officially, the airport was opened for civil operation on May 18, 1995. Since November 1, 1996 the airport is authorized for operation under the IFR rules.

In 2002, the City of Pardubice became the only proprietor and shareholder of EBA a.s.

Since its opening the airport is being used especially for the General Aviation flights. Charter flights for travel agencies in summer season are important part of airport air traffic. Synthesia Travel Agency organized first charter flights in 1996 to Bulgaria and Greece. Regular tourist flights from Pardubice date back to 2000 when the Fischer Travel Agency operated first charter flights from the airport to Mallorca. In year 2005 the offer of summer destinations was amended by Tunis with EXIM Tours and FIRO tour travel agencies, Crete by FIRO tour travel agency, Djerba by  Sunny Days travel agency and  Bulgaria with VVV tour and Alexandria agencies. Montenegro was then another destination added for summer season 2006 by Kovotour+ agency. Antalya and Rhodos are new destinations added to offer for season 2007 to increase number of offered destinations to 8.

In addition to these summer charters flights for Russian travel agencies transporting Russian tourists to the Czech Republic represent a highly important part of airport air traffic. Aircraft like B-737-300,400,500,800, B-757-200, Tu-204,Tu-214, Tu-154M ,Yak-42D.are operated for these flights and served by handling company.

Since its first days the airport is also used for all cargo flights. Airport can accept and served can be all cargo aircraft like Il-76, An-12, C-130. First 6 flights were performed to Pardubice with An-124 heavy cargo aircraft in the year 2005.

Opening of the airport for the civil air traffic started a long-term process during which existence and presence of a regional international airport in Pardubice comes to be known to the public of civil air transportation.