Background: Intralesional vitamin D3 has recently emerged as a new treatment for cutaneous warts. The use of the measles, mumps, and rubella (MMR) vaccine for this purpose is an established modality. However, relevant data on the efficacy of either the MMR vaccine or vitamin D3 as immunotherapy for cutaneous warts in the pediatric population are limited. Objectives: To compare the efficacy and safety of intralesional injections of MMR vaccine to intralesional injections of vitamin D3 in children aged 8-16 years with multiple warts. Methods: A total of 74 children were randomly allocated into two groups. Group A patients received intralesional MMR vaccine into the largest wart, and group B received intralesional vitamin D3 into the largest wart. The injections were repeated every 4 weeks until clearance or for a maximum of three treatments. After the last injection, children were followed up every 2 weeks for 3 months, and at the sixth month, a final clinical assessment was conducted. Results: Of 74 children, 60 completed the study, with 30 children in each group. Complete clearance of the injected wart was observed in 26 (86.67%) patients in the MMR group (group A) and 23 (76.7%) patients in the vitamin D3 group (group B). Distant warts cleared in 23 (76.7%) patients in group A compared to 20 (66.6%) patients in group B. There was no significant difference between groups. No recurrence was seen in group A, whereas two (6.6%) children in group B exhibited recurrence in the ensuing 6-month follow-up. The most common adverse events were injection site pain and swelling. Conclusion: Both intralesional MMR and vitamin D3 are safe, generally well-tolerated, and equally effective in children for the treatment of cutaneous warts.