Skopje Airport uses one terminal common to all flights. The building is very small but well designed. After security check, expect a shortage of seats at times when multiple planes depart at once.
Orientation is easy and distances within the terminal very short.
Passport control on arrival is efficient and waiting times tend to be in the 10-20 minute range.
Transfer between flights
Skopje is not a typical transfer airport. Most transfers are not guaranteed, i.e. travellers create their own transfer from two independent tickets.
Even if you don't have checked baggage, you must always go through passport control upon arrival, walk out and go through passport and security again back to the transit area.
Usually the whole procedure takes 20 to 40 minutes.