OBJECTIVE Oral lichen plans (OLP) is a potentially malignant inflammatory mucocutaneous disease. CD133 is an investigated surface marker for cancer stem-like cells (CSCs) that may be involved in tumor initiation in head and neck carcinomas. We compared short-term clinical effectiveness of topical pimecrolimus as selective inflammatory cytokine release inhibitor with betamethasone cream for erosive/atrophic OLP and investigated the influence of this therapy on CD133 expression. METHODS Thirty patients were randomly assigned into two equal groups to receive topical pimecrolimus (group I) or betamethasone (group II) four times daily for 4 weeks. A marker lesion in each patient were assessed at baseline using clinical score (CS) and visual analog scale (VAS) then at 1, 2, and 4 weeks and after 4 weeks of treatment-free period. CD133 expression was detected in pre- and post-treatment immunostained sections. RESULTS Both drugs showed a reduction in CS, VAS, and CD133 expressions after treatment termination (p < 0.001). Pimecrolimus-treated lesions showed significant higher 1st week reduction in severity (33.1% (22.2)), pain score (57.53% (14.27)), less recurrence in follow-up period and less CD133 expression by the end of the 1st 4 weeks compared with betamethasone. CONCLUSIONS Pimecrolimus showed earlier clinical response and less recurrence rate compared with standard topical corticosteroid in symptomatic OLP lesions, and both treatment reduced CD133-positive CSC population. CONCLUSIONS The study proved the benefits of topical pimecrolimus in early management of painful lesions of OLP and its ability to inhibit CSCs, suggesting a possible role in reducing risk of malignant transformation.