This study assessed the efficacy of antimicrobial photodynamic therapy (PDT) using a 650 nm diode laser combined with methylene blue (MB) as a photosensitizer to inhibit the growth of Candida albicans (C. albicans). Oral samples were collected from 75 patients diagnosed with oral thrush. C. albicans was isolated and identified using traditional methods and the VITEK 2 YST system. Samples (n = 25) were divided into five groups: Group 1 (control, n = 5) consisted of C. albicans suspensions in saline; Group 2 (n = 5) treated with nystatin; Group 3 (n = 5) exposed to a 650 nm diode laser in continuous mode at 200 mW for 300 seconds; Group 4 (n = 5) treated with 650 nm laser and MB as a photosensitizer; Group 5 (n = 5) exposed to the laser in combination with nystatin. Statistical analysis using ANOVA, Dunnett’s t-test (P = 0.05), and LSD (P = 0.001) revealed significant differences in C. albicans counts pre- and post-treatment. Group 5 showed the most significant reduction in C. albicans, followed by Group 4, while Groups 2 and 3 showed the least variation. The findings suggest that PDT using a 650 nm diode laser with methylene blue (in continuous mode at 200 mW for 300 seconds) effectively reduced the prevalence of C. albicans.