Managing the transit vessel traffic in the Strait of Istanbul is a highly complex operation since vessels, weather and water conditions, and a set of regulations affect its operation significantly. At the present time, the Vessel Traffic Services (VTS) operators manage the traffic based on some fundamental rules. After discussions with the VTS, in this report, we present a mathematical formulation of the scheduling process currently in place and validate it by comparing its results with scheduling decisions made by the operators in some days of 2005. The results are highly promising. The fundamental philosophy of the algorithm is to schedule the vessels with highest waiting time first while giving priority to large vessels carrying dangerous cargo. Our goal has been to incorporate the algorithm into a simulation model designed to be used for risk analysis purposes. The proposed algorithm can be slightly altered and used for traffic scheduling in other waterways as well.