Modified backstepping control is proposed for an under-actuated rotary double inverted pendulum. The system has actuated rotary base joint with which two unactuated links are attached. The proposed control design is a three step process for de-coupled system model. In the first stage, a backstepping controller is designed for each of the active and passive joints. In the second stage, compensation is introduced in the respective control efforts to cater for uncertain terms based on Lyapunov function for each joint. Finally, the controllers obtained in the two stages are combined to form a total control law. The performance of the proposed control scheme is evaluated by convergence analysis and simulations.