Purpose:To quantify daily set‐up variations in fractionated proton therapy of ocular melanomas, and to assess the effect on the fidelity of delivered distribution to the plan.Methods:In a typical five‐fraction course, daily set‐up is achieved by matching the position of fiducial markers in orthogonal radiographs to the images generated by treatment planning program. A patient maintains the required gaze direction voluntarily, without the aid of fixation devices. Confirmation radiographs are acquired to assess intrafractional changes. For this study, daily radiographs were analyzed to determine the daily iso‐center position and apparent gaze direction, which were then transferred to the planning system to calculate the dose delivered in individual fractions, and accumulated dose for the entire course. Dose‐volume metrics were compared between the planned and accumulated distributions for the tumor and organs at risk, for representative cases that varied by location within the ocular globe.Results:The analysis of the first set of cases (3 posterior, 3 transequatorial and 4 anterior tumors) revealed varying dose deviation patterns, depending on the tumor location. For anterior and posterior tumors, the largest dose increases were observed in the lens and ciliary body, while for the equatorial tumors, macula, optic nerve and disk, were most often affected. The iso‐center position error was below 1.3 mm (95%‐confidence interval), and the standard deviation of daily polar and azimuthal gaze set‐up were 1.5 and 3 degrees, respectively.Conclusion:We quantified interfractional and intrafractional set‐up variation, and estimated their effect on the delivered dose for representative cases. Current safety margins are sufficient to maintain the target coverage, however, the dose delivered to critical structures often deviates from the plan. The ongoing analysis will further explore the patterns of dose deviation, and may help to identify particular treatment scenarios which are at a higher risk for such deviations.