An increase of the deceleration in high-speed and high-density train operations degrades riding comfort and frequently causes wheel skids. This requires an introduction of the control technology to upgrade the control performance of brake systems on railway vehicles. We are now studying control methods for a mechanical brake that uses friction and pneumatic pressure, including nonlinear elements as the basis of a brake force. Furthermore, the system itself has certain “dead time,” which is not negligible and makes control difficult. One of our targets is to develop a brake control device that can control the deceleration in accordance with a decelerating pattern that optimizes the riding comfort of trains and prevents wheel skids. In this paper, a design method of the controller for the deceleration tracking control and the system compensating the dead time are proposed. Finally, the effects of them are confirmed through computer simulations and experimental results on a dynamo test stand.