BACKGROUND Despite the numerous studies on the use of purified protein derivative (PPD), a protein extracted from Mycobacterium tuberculosis, in verruca vulgaris, there is no standardized regimen, and efficacy of single versus multiple injections has not been compared. METHODS This is a randomized, open-label, superiority trial. Sixty-six patients with at least three warts in two different anatomic sites were randomized into two groups: a single injection (n = 29) and multiple injection (n = 29) groups. Patients were treated every 2 weeks until a maximum of six sessions. RESULTS Multiple injections (79.3%) showed superior clearance rates compared to a single injection of PPD (58.6%) (P-value = 0.0236). Multiple injections also exhibited faster clearance at each time point (P = 0.048). Pain was statistically more significant in the multiple injection group (P = 0.0005). There was no statistically significant difference in incidence of adverse events (P = 0.1795). Amongst all cleared patients in both groups, there were no recurrences after 6 months. CONCLUSIONS Multiple injections of warts with PPD cleared more patients with multiple common warts than the use of single injections at the end of 12 weeks and were faster in clearing patients at every time point. Single injection was better tolerated than multiple injections. Both treatments exhibited similar safety profiles and recurrence rates.