In a networked control system (NCS), time delays, uncertainties, packet losses, and exogenous disturbances seriously affect the control performance. To solve these problems, a modified disturbance suppression configuration of NCS was built. In the configuration, a proportional–integral observer (PIO) reproduces the state of a plant and reduces the observation error; an equivalent input disturbance (EID) estimator estimates and compensates for the disturbance in the control input channel. The stability conditions of the NCS are given by using a linear matrix inequality, and the gains of the PIO and state feedback controller are obtained. Numerical simulation results and an application of a magnetic levitation ball system verifies the effectiveness of the presented method. Comparison with the conventional PIO and EID methods shows that the presented method reduced the tracking error to about one-fifth and two-thirds of their original values, respectively. This demonstrates the validity and superiority of the presented method.