Background: Denture stomatitis is a common inflammatory condition in denture wearers primarily associated with Candida species. Conventional antifungal therapies are often limited by adverse side effects, high cost, and emerging drug resistance. Objective: To evaluate and compare the clinical efficacy of two herbal formulations - a ginger mouthwash and a combination ginger and yarrow mouthwash - against standard Nystatin suspension in patients with Type II denture stomatitis. Methods: In this double-blind, randomized clinical trial, 59 patients with Type II denture stomatitis were allocated to three intervention groups: ginger mouthwash, ginger–yarrow mouthwash, or Nystatin oral suspension. Palatal erythema was photographically evaluated on days 0, 7, 14, and 21. Surface area of erythema was quantified using ImageJ software. Inter- and intra-group differences were analyzed via one-way ANOVA and repeated-measures ANOVA, with statistical significance set at P < 0.05. Results: All three treatment regimens demonstrated a statistically significant reduction in palatal erythema over the 21-day period (P < 0.001). However, the Nystatin group achieved a significantly greater reduction in erythema area compared to both herbal mouthwash groups on days 7 and 14 (P < 0.05). By day 21, the difference between Nystatin and the herbal interventions was marginally significant (P = 0.054). Conclusion: While ginger and ginger–yarrow mouthwashes significantly reduce palatal inflammation, Nystatin suspension demonstrates superior speed and efficacy in the treatment of Type II denture stomatitis.