Robust optimization has been shown to be effective for stabilizing treatment planning in intensity modulated proton therapy (IMPT), but existing algorithms for the optimization process is time‐consuming. This paper describes a fast robust optimization tool that takes advantage of the GPU parallel computing technologies. The new robust optimization model is based on nine boundary dose distributions — two for ±range uncertainties, six for ±set‐up uncertainties along anteroposterior (A‐P), lateral (R‐L) and superior‐inferior (S‐I) directions, and one for nominal situation. The nine boundary influence matrices were calculated using an in‐house finite size pencil beam dose engine, while the conjugate gradient method was applied to minimize the objective function. The proton dose calculation algorithm and the conjugate gradient method were tuned for heterogeneous platforms involving the CPU host and GPU device. Three clinical cases — one head and neck cancer case, one lung cancer case, and one prostate cancer case — were investigated to demonstrate the clinical feasibility of the proposed robust optimizer. Compared with results from Varian Eclipse (version 13.3), the proposed method is found to be conducive to robust treatment planning that is less sensitive to range and setup uncertainties. The three tested cases show that targets can achieve high dose uniformity while organs at risks (OARs) are in better protection against setup and range errors. Based on the CPU + GPU heterogeneous platform, the execution times of the head and neck cancer case and the prostate cancer case are much less than half of Eclipse, while the run time of the lung cancer case is similar to that of Eclipse. The fast robust optimizer developed in this study can improve the reliability of traditional proton treatment planning in a much faster speed, thus making it possible for clinical utility.