Introduction: Many therapeutic modalities have been used for management of plantar warts; however, no optimal treatment with high efficacy and no or low recurrence has been explored to date. Intralesional immunotherapy has shown promising results in the treatment of different types of warts. Here we compare the efficacy of Candida albicans-specific antigen versus measles, mumps, and rubella (MMR) vaccine for treatment of plantar warts by intralesional injection. Methods: Sixty patients with refractory or recurrent plantar warts were randomly divided into two equal groups. Group A was treated with C. albicans antigen and Group B with MMR vaccine. Both groups were injected intralesionally in a single wart every 3 weeks until complete clearance of the wart or for a maximum of five sessions. The patients were followed up for an additional 2 months. Results: C. albicans antigen yielded a statistically significant higher cure rate (80.0%) than MMR vaccine (26.7%) in the treatment of plantar warts through a mean of 3.98 sessions versus 4.24 sessions, respectively (p = 0.002), and both modalities were well tolerated, with no remarkable side effects and no recurrence in cured patients during follow-up. Conclusions: Intralesional C. albicans antigen injection is an easy and effective treatment tool for plantar warts, even resistant and recalcitrant ones, with no post-procedural downtime and only transient occasional side effects. MMR vaccine is thought to be less effective.