This paper describes the method for stabilizing and trajectory tracking of Self Erecting Single Inverted Pendulum (SESIP) using Linear Quadratic Regulator (LQR). A robust LQR is proposed in this paper not only to stabilize the pendulum in upright position but also to make the cart system to track the given reference signal even in the presence of disturbance. The control scheme of pendulum system consists of two controllers such as swing up controller and stabilizing controller. The main focus of this work is on the design of stabilizing controller which can accommodate the disturbance present in the system in the form of wind force. An optimal LQR controller with well tuned weighting matrices is implemented to stabilize the pendulum in the vertical position. The steady state and dynamic characteristics of the proposed controller are investigated by conducting experiments on benchmark linear inverted pendulum system. Experimental results prove that the proposed LQR controller can guarantee the inverted pendulum a faster and smoother stabilizing process with less oscillation and better robustness than a Full State Feedback (FSF) controller by pole placement approach. © 2013 The Authors. Published by Elsevier Ltd.