Path following control of underactuated autonomous vessels remains a challenging issue in recent years due to its inherent underactuation and nonlinearities as well as the widely existing disturbances in the marine environment. In order to accommodate all the difficulties simultaneously, a novel extended state Kalman filter, which adopts the idea of extended state observer in estimating and compensating system lumped disturbance and optimizes the filter gain in a real-time fashion using Kalman filter technique, is constructed to estimate system states and disturbances in the presence of model uncertainties and measurement noise. Based on the estimated states and disturbances, an enhanced model predictive controller is proposed to steer the underactuated autonomous vessels along a predefined path at a desired speed after considering system state and input constraints. Simulation results have proved the superiority of extended state Kalman filter over traditional extended state observer and extended Kalman filter under various disturbance and noise scenarios. Moreover, the comparison results with conventional proportion-integration-differentiation controller have demonstrated the feasibility and efficacy of the proposed extended state Kalman filter-based model predictive controller in both set-point tracking and disturbance rejection.