This paper deals with a robust control problem for a ball and beam system with an uncertainty. At first, we clarify the effect of a measurement error in the beam rotational angle and its differential value. It is expressed as additional terms in the state and input matrix of the state equation, which is called as a structured uncertainty. For this system, a robust tracking controller and a robust state observer are applied. Both components are designed based on a robust control, which is called guaranteed cost control. This is a kind of cost minimization method for designing problem of a linear feedback system. The controller is obtained as the solution of the matrix algebraic Riccati like equation, which is referred to as stochastic algebraic Riccati equation. The nominal system performance is degraded due to the influence of the uncertainty, but it is able to design a system with robustness for disturbance. Next, we consider the design problem of a state observer to estimate all state variables form the output signal easy to measure, like rotation angle of the beam. For the design problem of the state observer, we consider dual problem of the original system. Consequently, our proposed system estimates the whole state vector, and using estimated state values, it controls the ball to the desired position. Both components have robustness for the uncertainty. Numerical result shows the validity of our proposed method.