Passenger check-in process is the beginning of the journey along to flight just after entering the airport. Qualification of the service given in check-in counters doesn’t differ from assignment type, but counter queue and other related parameters are affected by assignment type. During the check-in process that is generally provided by ground handling firms, parameters like average waiting time in queue, average time in the system, resource utilization are not taken into consideration. On the other hand airport administrations are becoming more aware of minimizing delays and using capacity effectively in the recent days. Considering entire parameters of the existing queue systems is providing us to determine delays and to increase efficiency on the way to optimizing entire system. In the study data is collected from the Ataturk Airport international departure check-in counters on peak hours. Check-in counter assignments are observed in two types as common use and flight based use. Collected data is used to develop a simulation model in ArenaTM. Via developed simulation model, delays in the counter queues are examined and reasons are explained. Besides different scenarios are analyzed in order to increase system efficiency.