This study analyzes the uncertainty of the compensation method of a sensing error of three-DOF measuring system. This compensation method utilizes a reference coordinate system using a three point by moving a position of an endpoint of a three-DOF manipulator. The coordinate transformation between the three-DOF manipulator and the measuring system is identified by the reference coordinate system. According to the concept of this compensation method, each positioning error at any position of the end-point of the manipulator is derived. Uncertainty analyses of the compensation values on the basis of sensitivity analysis and Monte Carlo simulation are used to investigate a feasibility and effectiveness of the compensation method.