Purpose The purpose of this study was to investigate daily repositioning accuracy by analyzing inter‐ and intra‐fractional uncertainties associated with patients treated for intracranial or base of skull tumors in a compact proton therapy system with 6 degrees of freedom (DOF) robotic couch and a thermoplastic head mask indexed to a base of skull (BoS) frame. Materials and methods Daily orthogonal kV alignment images at setup position before and after daily treatments were analyzed for 33 patients. The system was composed of a new type of thermoplastic mask, a bite block, and carbon‐fiber BoS couch‐top insert specifically designed for proton therapy treatments. The correctional shifts in robotic treatment table with 6 DOF were evaluated and recorded based on over 1500 planar kV image pairs. Correctional shifts for patients with and without bite blocks were compared. Results Systematic and random errors were evaluated for all 6 DOF coordinates available for daily vector corrections. Uncertainties associated with geometrical errors and their sources, in addition to robustness analysis of various combinations of immobilization components were presented. Conclusions Analysis of 644 fractions including patients with and without a bite block shows that the BoS immobilization system is capable of maintaining intra‐fraction localization with submillimeter accuracy (in nearly 83%, 86%, 95% of cases along SI, LAT, and PA, respectively) in translational coordinates and subdegree precision (in 98.85%, 98.85%, and 96.4% of cases for roll, pitch, and yaw respectively) in rotational coordinates. The system overall fares better in intra‐fraction localization precision compared to previously reported particle therapy immobilization systems. The use of a mask‐attached type bite block has marginal impact on inter‐ or intra‐fraction uncertainties compared to no bite block.