Ever since the emergence of magnetic resonance (MR)-guided radiotherapy, it is important to investigate the impact of the magnetic field on the dose enhancement in deoxyribonucleic acid (DNA), when gold nanoparticles are used as radiosensitizers during radiotherapy. Gold nanoparticle-enhanced radiotherapy is known to enhance the dose deposition in the DNA, resulting in a double-strand break. In this study, the effects of the magnetic field on the dose enhancement factor (DER) for varying gold nanoparticle sizes, photon beam energies and magnetic field strengths and orientations were investigated using Geant4-DNA Monte Carlo simulations. Using a Monte Carlo model including a single gold nanoparticle with a photon beam source and DNA molecule on the left and right, it is demonstrated that as the gold nanoparticle size increased, the DER increased. However, as the photon beam energy decreased, an increase in the DER was detected. When a magnetic field was added to the simulation model, the DER was found to increase by 2.5–5% as different field strengths (0–2 T) and orientations (x-, y- and z-axis) were used for a 100 nm gold nanoparticle using a 50 keV photon beam. The DNA damage reflected by the DER increased slightly with the presence of the magnetic field. However, variations in the magnetic field strength and orientation did not change the DER significantly.