Background: Cutaneous warts are a common dermatological condition caused by the human papillomavirus (HPV). They are often challenging to treat due to their persistence and tendency to recur. Multiple treatment options exist, but none are universally effective, and many have limitations, such as pain, side effects, or high recurrence rates. Immunotherapy has emerged as a promising approach, utilizing agents like Bacillus Calmette-Guérin (BCG) vaccine and vitamin D3 to modulate the immune response against warts. The intralesional route is particularly attractive, as it can stimulate a localized immune response, potentially improving treatment efficacy and reducing systemic side effects. This study aims to compare the efficacy and safety of intralesional BCG vaccine versus intralesional vitamin D3 in the treatment of cutaneous warts, with a focus on evaluating clinical response, adverse effects, and recurrence rates. Objective: To compare the efficacy and safety of intralesional Bacillus Calmette-Guérin (BCG) vaccine versus intralesional vitamin D3 in the treatment of cutaneous warts. Methods: A randomized comparative prospective study was conducted involving 112 patients with cutaneous warts. Patients were divided into two groups: Group A received intralesional BCG vaccine (0.1 ml) and Group B received intralesional vitamin D3 (0.2 ml, 15 mg/ml). Treatments were administered at 2-week intervals for a total of 4 sessions. Efficacy was assessed based on reduction in wart size, complete clearance, and grading of response. Results: At the final follow-up (8th week), complete response was observed in 37.5% of patients in the BCG group and 42.86% in the vitamin D3 group. Palmoplantar warts showed the best response to both treatments. Vitamin D3 demonstrated superior efficacy in clearing all types of warts compared to BCG vaccine. The vitamin D3 group experienced fewer side effects, with pain at the injection site being the most common (71.43%). The BCG group reported more diverse side effects, including erythema (67.86%), swelling (60.71%), and ulceration (53.57%). Conclusion: Intralesional vitamin D3 showed superior efficacy and a better safety profile compared to intralesional BCG vaccine in the treatment of cutaneous warts. Vitamin D3 demonstrated particular effectiveness in clearing palmoplantar warts and resulted in higher patient satisfaction due to its lasting clinical effects and reduced recurrence rate.