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The optimal operation of rail vehicle minimizing total energy consumption is discussed in this paper. Many works on the application of the energy storage devices to trains were reported, however, they did not deal enough with the optimality of the control of the devices. The authors have developed the mathematical model based on a general optimization technique, Sequential Quadratic Programming. The proposed method can determine the optimal acceleration/deceleration and current commands at every sampling point under fixed conditions of transfer time and distance. Using the proposed method, simulations were implemented in some cases. The electric double layer capacitor (EDLC) is assumed as an energy storage device in our study, because of its high power density etc. The trend of optimal solutions such as values of control inputs and energy consumption is finally discussed.