Context: Warts are caused by Human papilloma virus. Various treatment modalities are present such as electrocautery, chemical cautery and cryotherapy. Immunotherapy is emerging as new treatment option which acts by enhancing the cell-mediated immunity against HPV. Aims: To compare the therapeutic efficacy and safety of intralesional 5-Fluorouracil (5-FU) versus intralesional Vitamin D3 in cutaneous warts. Settings and Design: Hospital-based interventional prospective study. Methods and material: We selected 176 patients with cutaneous warts and randomly divided into two groups of 88 patients each. Group A were treated with intralesional 5-Fluorouracil (50mg/ml) and Group B were treated with intralesional Vitamin D3 (6lac units 15mg/ml). The procedure was repeated at 2 weeks interval up to 5 times or till clearance of lesion. The side effects were noted. Statistical analysis used: Statistical Package for Social Sciences (SPSS) software version 25.0. The results were analysed using Chi-Square test and Student’s t test. p value of <0.05 was considered significant. Results: At the end of therapy, complete cure rates obtained were 82% (72/88) in 5-FU treated patients (Group A) and 64% (56/88) in Vitamin D3 treated patients (group B). Conclusion: Intralesional 5-fluorouracil is worth considering as a therapeutic option for the treatment of viral wart is safe, cost- effective, efficacious and lacks serious side-effects.