This study aimed to evaluate the clinical beam commissioning results and lateral penumbra characteristics of our new pencil beam scanning (PBS) proton therapy using a multi‐leaf collimator (MLC) calculated by use of a commercial Monte Carlo dose engine. Eighteen collimated uniform dose plans for cubic targets were optimized by the RayStation 9A treatment planning system (TPS), varying scan area, modulation widths, measurement depths, and collimator angles. To test the patient‐specific measurements, we also created and verified five clinically realistic PBS plans with the MLC, such as the liver, prostate, base‐of‐skull, C‐shape, and head‐and‐neck. The verification measurements consist of the depth dose (DD), lateral profile (LP), and absolute dose (AD). We compared the LPs and ADs between the calculation and measurements. For the cubic plans, the gamma index pass rates (γ‐passing) were on average 96.5% ± 4.0% at 3%/3 mm for the DD and 95.2% ± 7.6% at 2%/2 mm for the LP. In several LP measurements less than 75 mm depths, the γ‐passing deteriorated (increased the measured doses) by less than 90% with the scattering such as the MLC edge and range shifter. The deteriorated γ‐passing was satisfied by more than 90% at 2%/2 mm using uncollimated beams instead of collimated beams except for three planes. The AD differences and the lateral penumbra width (80%–20% distance) were within ±1.9% and ± 1.1 mm, respectively. For the clinical plan measurements, the γ‐passing of LP at 2%/2 mm and the AD differences were 97.7% ± 4.2% on average and within ±1.8%, respectively. The measurements were in good agreement with the calculations of both the cubic and clinical plans inserted in the MLC except for LPs less than 75 mm regions of some cubic and clinical plans. The calculation errors in collimated beams can be mitigated by substituting uncollimated beams.