Candida albicans adhesion and proliferation on denture bases may lead to denture stomatitis, which is a common and recurrent problem in denture wearers. The goal of this study was to assess the inhibitory effect of thymoquinone incorporated in the polymethyl methacrylate denture base material against Candida albicans. Eighty acrylic resin specimens were fabricated and divided into eight groups (n = 10) according to thymoquinone concentrations of 0.5%, 1%, 1.5%, 2%, 2.5%, 3%, and 5% of acrylic powder. Two methods were used to evaluate the effect of thymoquinone on Candida albicans: the slide count and the serial dilution test. A multivariate analysis of variance (MANOVA) and the post-hoc Tukey’s Honestly Significant Difference (HSD) test were performed to compare the difference of means between the observations taken at various intervals with baseline. The p value was statistically significant at ≤0.05. According to the slide count and the serial dilution test, the mean number of adhered Candida albicans in the control group was 5436.9 ± 266 and 4691.4 ± 176.8; however, this number dramatically decreased to 0 ± 0 and 32.4 ± 1.7 in group 8 (concentration 5%). These results suggest that the incorporation of thymoquinone into the acrylic resin denture base material might be effective in preventing Candida albicans adhesion.