Purpose: To verify a clinical pencil (PB) beam dose calculation algorithm for scanned beam intensity modulated proton therapy (IMPT), using TOPAS (TOol for PArticle Simulation), a GEANT4 based Monte Carlo (MC) simulation system. Methods: Seven patients, previously treated with IMPT for various treatment sites and prescriptions, were selected from our patient database. Proton fluence maps of the treated plans were exported for each field from our clinical treatment planning system (ASTROID) and imported to TOPAS along with the patient and beam geometry. The absolute dose distribution of each individual beam was calculated and compared to the PB algorithm‐based calculation from ASTROID. Results: The differences observed in mean and median target doses were less than ±1% for all cases, while D02 and D98 (surrogates for maximum and minimum dose values respectively) differed by less than ±3% for the majority of beams. Differences in the mean dose for the organs at risk (OARs) ranged from −8.9% to 3.7%, with reference to MC calculation, with an average over all the OARs of −0.1%, indicating no systematic over‐or under‐estimation of the dose by the PB algorithm. 3D gamma analysis (2%/2mm) for the PB to MC dose comparison resulted in an average 95.2% (±5.0) of the target volume having an absolute gamma value equal or less than 1 and 99.2% (±1.2%) equal or less than 2. For the healthy tissue receiving at least 5% of the target mean dose, the corresponding percentages were 99.6% (±0.3%) and 99.9% (±0.1%). Conclusion: We have clinically implemented MC for IMPT plan recalculation. Our PB calculation algorithm for IMPT was found to be in overall good agreement with MC calculations. Clinically significant deviations in OAR mean dose can be attributed to lung tissue or bone anatomy in the beam path.