Our purpose was to establish the commissioning procedure of Monte Carlo modeling on a magnetic resonance imaging-guided radiotherapy system (MRIdian, Viewray Inc.) under a magnetic field of 0.345 T through experimental measurements. To do this, we sought (i) to assess the depth-dose and lateral profiles generated by the Geant4 using either EBT3 film or the BJR-25 data; (ii) to assess the calculation accuracy under a magnetic field of 0.345 T. The radius of the electron trajectory caused by the electron return effect (ERE) in a vacuum was obtained both by the Geant4 and the theoretical methods. The surface dose on the phantom was calculated and compared with that obtained from the film measurements. The dose distribution in a phantom having two air gaps was calculated and measured with EBT 3 film. (i) The difference of depth-dose profile generated by the Geant4 from the BJR-25 data was 0.0 ± 0.8% and 0.3 ± 1.5% for field sizes of 4.5 and 27.3 cm2, respectively. Lateral dose profiles generated by Geant4 agreed well with those generated from the EBT3 film data. (ii) The radius of the electron trajectory generated by Geant4 agreed well with the theoretical values. A maximum of ~50% reduction of the surface dose under a magnetic field of 0.345 T was observed due to elimination of the electron contamination caused by the magnetic field, as determined by both the film measurements and the Geant4. Changes in the dose distributions in the air gaps caused by the ERE were observed on the Geant4 and in the film measurements. Gamma analysis (3%/3 mm) showed a pass rate of 95.1%. Commissioning procedures for the MRI-guided radiotherapy system on the Geant4 were established, and we concluded that the Geant4 had provided high calculation accuracy under a magnetic field of 0.345 T.