Abstract: The increases of car ownership, population growth and urbanization have increased traffic congestion in many cities in the world. One of the alternatives to reduce congestion is application of congestion pricing. The aim of this research is to estimate the congestion cost of motorcycles and the impact of congestion pricing scheme on the generalized cost and speed of motorcycle to the city of Yogyakarta, Indonesia. The amount of the congestion pricing is the difference between generalized cost in free-flow speed and actual generalized cost in traffic jam condition. In this study, generalized costs of motorcycle from origin zone i to destination zone j consists of vehicle operating cost and travel time cost. This study shows that while the free-flow speed of motorcycle to the city of Yogyakarta is 45.45 km h^-1 bring on the generalized cost is IDR774 per trip, the actual speed in traffic jam condition is 12.57 km h^-1 produce the generalized cost is IDR1655 per trip, giving the congestion pricing of motorcycle to the city of Yogyakarta is IDR881 per trip. The impact of application of congestion pricing for motorcycles users will increase the vehicle speeds between 0.42-6.32% and decreases the generalized cost. Speed of vehicle will increase as 1.76 kmh^-1 in Malioboro Street. The amount of generalized cost of motorcycles will decrease IDR36 per trip (3.63%).