Construction of Zielona Góra Airport (a former military base) began in 1954, and it entered service on 10 October 1957. A Lim-6R, which is a Polish built MiG-17 is parked adjacent to the terminal, commemorating the airport's military origin.

Although the first passenger terminal opened in 1977, at least one passenger flight had already operated from the airport (on 21 July 1961, bringing Yuri Gagarin to Zielona Góra). The airport began service to and from Warsaw and Gdańsk in 1977; the first scheduled flights were twice weekly to Warsaw, and the Gdańsk route operated during the 1970s. It hosted twice-daily passenger service to Warsaw until September 2004, when state-owned LOT Polish Airlines discontinued the route after ownership changes at the airport. The army stopped using it as a military base, and dismantled some of its equipment.

The airport was rented to regional authorities in 2005, so its new owner could begin developing the airport. Shifts in the Polish airline market caused financial problems for LOT, and service to Warsaw was suspended because the airline could not obtain suitable mid-sized aircraft for the route.

At the end of 2005, two daily flights to Warsaw were operated by Jet Air; this was later reduced to one. The airport has had short-lived scheduled routes to Gdańsk, Kraków, and Dresden, and service to Warsaw operated via Poznań or Bydgoszcz. It operated charter service to southern Europe and Ukraine during the mid-2010s. In January 2017, it was announced that the airport's only scheduled route (to Warsaw Chopin Airport) would be transferred from SprintAir to LOT.

In December 2022 renderings of a new terminal building were published by an architect studio that won public tendering for the project.