There are 3 terminals at the airport, the Terminal 1, Terminal 2 and Terminal 3. The Terminal 1,2 deals with both international and domestic departures and arrivals, whereas the Terminal 3 serves general and business aviation. Transfer between these terminals is by either minibus or taxi. All flights from Shengen countries arrives at Terminal 2 (like Spain, Germany etc.) and all other flights (flights from non-Shengen countries like USA and UK) arrives there at the Terminal 1. New Terminal 2 last year opened is now offering great facilities and is made up of six buildings which will be brought into service at the beginning of January 2006, mainly deals with flights to and from the EU. By launching Terminal 2, Prague Airport has made a significant step in the effort to modernize its facilities, offer seamless handling and increase the transport capacity of the airport, which is becoming one of the major air hubs in Central and Eastern Europe. Terminal North 2 will start operating on 17 January. The new terminal will allow Prague Airport to handle another up to 4 million passengers a year. More planned investment linked to this terminal will help channel more visitors to Prague and double the number of passengers to around 20 million a year roughly over the next 12 years.

Terminal names are being simplified along with flight transfers.
Terminals for the traveling public:
Current name:Terminal North 1 (abbreviation TN1) New name: Terminal 1 (abbreviation T1)
Current name: Terminal North 2 (abbreviation TN2) New name: Terminal 2 (abbreviation T2)
Terminal for private flights:
Current name:Terminal South 2
New name: Terminal 3 General Aviation (abbreviation T3)