In this paper two important problems, i.e. Denial of Service (DoS) attack and saturated input, are considered for the TCP/AQM system. The first problem is modelled in a quantitative manner over the system dynamics. Then, Linear Matrix Inequality (LMI) condition for synthesising a Dynamic Output Feedback (DOF) controller with guaranteed cost approach is proposed. The second problem is inherently asymmetric, and a generalised sector condition is derived to obtain stability conditions based on quadratic Lyapunov functions. Sufficient conditions in terms of LMIs for designing the anti-windup compensator are then derived. By solving these LMIs, the controller matrices along with the less bound of the cost function and an appropriate anti-windup compensator are obtained. Through Network Simulator 3 (NS3) the efficiency of the theory is illustrated.