Background This study evaluates dose perturbations caused by nonradioactive seeds in clinical cases by employing treatment planning system-based Monte Carlo (TPS-MC) simulation. Methodology We investigated dose perturbation using a water-equivalent phantom and 20 clinical cases of prostate cancer (10 cases with seeds and 10 cases without seeds) treated at Fujita Health University Hospital, Japan. First, dose calculations for a simple geometry were performed using the RayStation MC algorithm for a water-equivalent phantom with and without a seed. TPS-independent Monte Carlo (full-MC) simulations and film measurements were conducted to verify the accuracy of TPS-MC simulation. Subsequently, dose calculations using TPS-MC were performed on CT images of clinical cases of prostate cancer with and without seeds, and the dose distributions were compared. Results In clinical cases, dose calculations using MC simulations revealed hotspots around the seeds. However, the size of the hotspot was not correlated with the number of seeds. The maximum difference in dose perturbation between TPS-MC simulations and film measurements was 3.9%, whereas that between TPS-MC simulations and full-MC simulations was 3.7%. The dose error of TPS-MC was negligible for multiple beams or rotational irradiation. Conclusions Hotspots were observed in dose calculations using TPS-MC performed on CT images of clinical cases with seeds. The dose calculation accuracy around the seeds using TPS-MC simulations was comparable to that of film measurements and full-MC simulations, with differences within 3.9%. Although the clinical impact of hotspots occurring around the seeds is minimal, utilizing MC simulations on TPSs can be beneficial to verify their presence.