In this study, the scheduling problem of air traffic controllers (ATCo) providing area control services in Turkey is discussed. Airspace is divided into multiple sectors, as controllers can control a limited number of aircraft in a given time period.The area control service provided for the flights at the en-route phase includes both of the transit and domestic flights.The traffic density in these sectors varies according to hourly zones, day-night hours and seasons. As the traffic density increases, the workload also increases. In addition, seasonal differences and weather conditions are factors that affect the workload. In the study, a two-stage mathematical model is proposed in order to balance the workload distribution of the controllers, considering the estimated traffic demand and weather conditions in the sectors. In the first stage, shift assignments were made to balance the total workload of the teams consisting of a certain number of people in a ten-day period. In the second stage, the controllers were scheduled to balance the workloads of the teams in each shift. In addition to the working conditions of the controllers such as work and rest hours, the difference of experienced and inexperienced ATCo is also considered.