A new control method is developed for position tracking control of a flexible, non-collocated system. The desired trajectory is specified for the free end of a flexible beam that moves along a horizontal track actuated by a linear motor. First, a system model is reformulated based on a pendulum with stiffness and dampening. Small angle approximations are used so that a linear model can be obtained. Next, variable structure control is chosen as the control method due to its seemingly robust nature. The sliding surface and feedback gains are designed using the developed model based on literature describing various variable structure control techniques. Simulations are then conducted to verify the control method and examine its robustness. Finally, the method is implemented on an actual system using a Kalman filter to estimate the states.