The airports of Kavala and Alexandroupolis serve a wide catchment area in Northern Greek periphery, offering air transport services to almost half a million habitants as well as to international tourists. The international passengers of Kavala airport are travelling mainly during the summer period with charter flights that impose high peaks in various subsystems of the airport terminal. The airport of Alexandroupolis mainly serves passengers of domestic flights that are usually accompanied by friends or relatives, leading to overcrowding of the corresponding waiting areas. The existence of the above passenger flows peculiarities, indicates the need for an appropriate design technique of the related airport terminal facilities. The scope of this paper is to describe such an approach, based on a simulation model that was used during the master plans of the above airports. The model simulates the flows of both departing and arriving passengers, distinguishing the intra and extra-Schengen flows so as to charge the various subsystems of the airport terminal accordingly, while emphasis was given in the investigation of the level of service offered in the departure lounges.