After it lost its military importance with the end of the Cold War, it served as a passenger airport for a few years at the turn of the millennium.

The Szymany Airport received international attention after it was discovered the airfield was used by the CIA in conjunction with a black site prison nearby in 2003.

From 2014 to 2015, the airport was rebuilt with high EU subsidies as part of the "Regional Operational Programme Warmia and Mazury 2007–2013".

The airport is situated 59 kilometres to the south of Olsztyn, at the border with more densely populated Mazowsze region.

Despite the eventual cessation of scheduled services between the aforementioned destinations, the airport is still operational as a flight school and general aviation airfield.

The resumption of flights would have required renovation and expansion of terminal facilities and the runway, costing some five to six million Polish Zloty.

The airport gained attention in the press in 2005, when it was alleged to have a connection with a so-called black site involved in the CIA's network of extraordinary renditions.

Flight records show that an airplane leased by the CIA flying from Kabul to Guantanamo Bay made a stop in Szymany.

Officials from the airport have confirmed that some of these flights bypassed normal customs-clearing procedures, and that during the time of these landings, the airport regularly received visits by cars bearing markings associated with the Stare Kiejkuty intelligence training school outside the nearby village of Stare Kiejkuty.

As recently as November, 2006, the European Parliament investigative commission led by Claudio Fava had been told, when asked for the flight logs of 11 specific flights observed to have transited through Szymany, that "[the records] have [not] been retained, have been faxed and destroyed, and finally said to have been saved in an unspecified place.

"[7] The commission report also quotes Szymany officials as confirming six occasions in 2002 and 2003 when Gulfstream jets bearing civilian registration numbers had landed at the airport, bypassing customs clearance.

In June 2008 a New York Times article claimed, citing unnamed CIA officers, that Khalid Sheikh Mohammed was held in a secret facility in Poland near Szymany Airport and it was there that he was interrogated and waterboarded before beginning to cooperate.

[8] In February 2010 Polish officials recanted previous denials, and admitted that at least six CIA flights passed through Szymany in 2003.

[9] Following several quiet years, ideas again come up to reconstruct the airport in order to resume passenger services.

An investment of 200 million was planned that included extension and renovation of the runway from 2000 to 2500 metres, aprons, taxiways and a brand new terminal.

EU funds would only be granted as long the reconstruction airport would be operative by the end of 2015, resulting in tight schedule for construction.

[13] In late October 2015, the airport finally signed an agreement with Polish airline Sprint Air.

The continues to service Berlin Tegel and Kraków thrice weekly, although with a slightly modified schedule.

Starting 17 June 2016, Adria Airways would operate a thrice-weekly connection to Munich onboard its CRJ aircraft.

Wizz Air is known for their all-Airbus fleet of A320s and A321s, meaning that a greater number of passengers can be served through the airport rather than with CRJs and Dash-8 aircraft alone.

[21] By mid-June 2016, LOT Polish Airlines opened bookings for a three-weekly service from Olsztyn to their hub Warsaw on board their 78-seated Bombardier Q400.

Running in the middle of the day, the service should deliver many connection options to other destinations within the LOT network.