The purpose of this paper is to introduce a new trajectory tracking controller applied to the Furuta pendulum; where the arm tracks a desired time-varying trajectory, while the pendulum remains regulated at the upward position. This controller is derived from the input-output feedback linearization technique. The rigorous analysis of the internal dynamics is presented, showing that the tracking error and the regulation error trajectories are uniformly ultimately bounded. Experimental results show the validity of the introduced theory. Additionally, a detailed experimental study is also presented, where a PID controller and an output tracking controller are compared with respect to the new algorithm, which presents the best performance.