Tolerance estimation problems are prevailing in engineering applications. For example, in modern robotics, it remains challenging to efficiently estimate joint tolerance, \ie the maximal allowable deviation from a reference robot state such that safety constraints are still satisfied. This paper presented an efficient algorithm to estimate the joint tolerance using sum-of-squares programming. It is theoretically proved that the algorithm provides a tight lower bound of the joint tolerance. Extensive numerical studies demonstrate that the proposed method is computationally efficient and near optimal. The algorithm is implemented in the JTE toolbox and is available at \url{https://github.com/intelligent-control-lab/Sum-of-Square-Safety-Optimization}.