A method for trajectory tracking accuracy analysis of a two-link flexible manipulator with lubricated revolute joint involving interval uncertainty is presented. In this method, first, fuzzy self-tuning proportion integration differentiation (PID) control is applied to track the desired tip trajectory of the manipulator. The absolute nodal coordinate formulation (ANCF) is employed for the finite element discretization of the flexible manipulator. And lubricated revolute joint is modeled based on the infinitely short journal bearing with Gümbel conditions. Second, uncertainty of clearance size is considered, and interval analysis method is applied. Numerical simulation is posted to investigate the cushioning effect of lubricants on the clearance and influence of uncertainty on control accuracy of the manipulator. The results show that the lubricants can improve the stability of motion and operation precision of the manipulator; however, uncertainty of the manipulator may reduce the control accuracy of the manipulator.