Purpose: Range compensators are used in both passive and active uniform scanning proton beams to conform proton dose to the target's distal boundary. The manufacturing accuracy of compensators has a direct effect on range uncertainty in proton beams. The purpose of the study is to investigate the thickness difference between manufactured and planned compensators and its effect on range uncertainty. Methods: We used a range compensator QA table with 2‐D motors and overhead 1D laser measurement tool to measure the compensator thickness. The QA device allows automatic multiple milling point measurements with minimal man‐hours, with export of QA results to a tabulated file for ease of data analysis. We recorded the QA results of over 12,000 points across over 500 different blue wax compensators and analyzed the thickness deviation from treatment planning with a histogram plot. Results: The average measured compensator thickness is about 0.03 mm less than the expected according to the treatment plans. The standard deviation is about 0.17 mm. Causes for thickness deviation of larger than 0.5 mm were investigated. The corresponding water equivalent range uncertainty of a compensator is similar to the physical thickness deviation because the blue wax has a relative stopping power ratio of 0.97. Some large deviations due to human errors were analyzed separately. Conclusion: The range uncertainty through the range compensator is dependent on the accuracy of the milling device and also the relative stopping power of the compensator material. It is recommended to use material with stopping power close to water for compensators to mitigate the errors in milling yet also to reduce the bulkiness of the compensator. The range uncertainty due to compensator thickness inaccuracy is estimated to be about 0.3 mm (2 sigma) in our clinic.