The purpose of this study is to evaluate the antimicrobial effect of Iranian mineral trioxide aggregate (IMTA) and NanoSilver-IMTA (NS-IMTA) at clinical concentrations against Porphyromonas gingivalis, a Gram-negative anaerobic black-pigmented bacterium that is strongly associated with acute symptoms and signs in endodontic infections. We combined NS (0.1 mg/mL) with IMTA at 6, 12 and 25% concentrations. To evaluate the antimicrobial effect, agar diffusion and broth dilution methods were used. The data were analyzed using one-way ANOVA and post hoc analysis. In the agar diffusion test, 12% and 25% NS-IMTA showed zones of inhibition against P. gingivalis, while IMTA and 6% NS-IMTA showed no zone. In the broth dilution assay, IMTA reduced the growth of P. gingivalis by 30.8% and 36.2% after 48h and 72 h, respectively. For 6% NS-IMTA, although the reduction in the number of viable bacteria was slightly higher than that of the IMTA after 72 h, there was no significant difference. After 48 h, IMTA containing 12% and 25% NS completely inhibited the proliferation of P. gingivalis. A statistically significance difference (p < 0.05) was found between IMTA and IMTA containing 12% and 25% NS. In Conclusions, NS-IMTA completely inhibits the proliferation of P. gingivalis in a dose-dependent manner that may have a significant effect in prognosis for root perforation.