Background Oral stomatitis is one of the common infections related to dentures (complete or partial), which is seen in the form of diffuse inflammation, mainly with Candida albicans. The aim of the present study was to investigate the antifungal effects of Hypericum perforatum nanoemulsion against Candida albicans. Materials and Methods The microdilution technique has been used in order to determine the antifungal effects of Hypericum perforatum nanoemulsion. The study has involved four groups: Hypericum perforatum oil, Hypericum perforatum nanoemulsion, distilled water as a negative control, and nystatin as a positive control. The first concentration of nanoemulsion in which no clear fungal growth was observed in the culture medium has been considered as the Minimum Inhibitory Concentration (MIC) and the first concentration in which the fungal growth was completely stopped and no fungal growth was observed in the culture medium has been considered as the Minimum Fungicide Concentration (MFC). One-way Analysis of Variance (ANOVA) has been employed to compare the results between the groups. Tukey's post-hoc test has been used to make comparisons between the groups. The significance level has been considered at less than 0.05. Results Both Hypericum perforatum oil and Hypericum perforatum nanoemulsion have been found to exhibit good antifungal activity against Candida albicans. The MIC and the MFC of the nanoemulsion form have been found to be lower than the non-nanoemulsion form (P<0.05). Among the studied groups, the nystatin group had been found to have the best effect (P<0.05). Conclusion Considering the different antifungal mechanisms and also the different resistance mechanisms of nystatin and Hypericum perforatum nanoemulsion, the prepared nanoemulsion can be used to treat and reduce the population of nystatin-resistant Candida albicans strain. However, the efficiency of these materials needs to be confirmed in larger studies on resistant strains.