Background Many therapeutic modalities were reported for the treatment of warts; however, no single treatment is completely effective. Objective To evaluate the efficacy of intralesional injection of MMR vaccine vs vitamin D in treatment of warts. Patients and Methods A total of 60 patients were included in the study divided into two groups. Group A received intralesional MMR vaccine into largest wart, and group B received intralesional vitamin D3 into each lesion with maximum of five warts treated in one session. A maximum of six sessions was done every 3 weeks in both groups. Follow‐up was done for 6 months for any recurrence. Results In group A: complete response in 80%, partial response in 6.67%, minimal response in 6.67%, and no response in 6.67% of patients. About 60% of patients with multiple warts showed complete clearance of distant untreated warts. In group B: complete response in 66.7%, partial response in 6.67%, minimal response in 20%, and no response in 6.67% of patients. There was no significant difference between both groups. No recurrence was observed in both groups in the follow‐up period. Conclusions Immunotherapy by both intralesional MMR vaccine and vitamin D3 is simple, well‐tolerated, effective, and cost‐benefit modalities for the treatment of warts.