In this paper the numerical method based on Monte-Carlo techniques is utilized for the analysis of the flying height measurement uncertainty. In the current flying height tester, the prediction of error is the main concern in order to assure the attainable precision. In previous study, a simplified analytical method is normally used and it may not provide the accurate results of the error prediction especially when the amount of the flying height values becoming as low as sub-5 nm. In this paper, instead of using the analytical method for error analysis, the numerical method based on Monte-Carlo techniques is utilized. Our simulation results show that the measurement uncertainty is mainly from the variation in the optical constants of the DLC layer. They also show that the increasing of standard deviation of the optical constants of DLC layer causes the higher measurement uncertainty.