In nanoparticle (NP)-enhanced orthovoltage radiotherapy, bone scatter affected dose enhancement at the skin lesion in areas such as the forehead, chest wall, and knee. Since each of these treatment sites have a bone, such as the frontal bone, rib, or patella, underneath the skin lesion and this bone is not considered in dose delivery calculations, uncertainty arises in the evaluation of dose enhancement with the addition of NPs in radiotherapy. To investigate the impact of neglecting the effect of bone scatter, Monte Carlo simulations based on heterogeneous phantoms were carried out to determine and compare the dose enhancement ratio (DER), when a bone was and was not present underneath the skin lesion. For skin lesions with added NPs, Monte Carlo simulations were used to calculate the DER values using different elemental NPs (gold, platinum, silver, iodine, as well as iron oxide), in varying NP concentrations (3–40 mg/mL), at two different photon beam energies (105 and 220 kVp). It was found that DER values at the skin lesion increased with the presence of bone when there was a higher atomic number of NPs, a higher NP concentration, and a lower photon beam energy. When comparing DER values with and without bone, using the same NP elements, NP concentration, and beam energy, differences were found in the range 0.04–3.55%, and a higher difference was found when the NP concentration increased. By considering the uncertainty in the DER calculation, the effect of bone scatter became significant to the dose enhancement (>2%) when the NP concentration was higher than 18 mg/mL. This resulted in an underestimation of dose enhancement at the skin lesion, when the bone underneath the tumour was neglected during orthovoltage radiotherapy.