Introduction: Chronic Plantar Ulcer of Leprosy (CPUL), one of the debilitating disabilities and complications, poses a treatment challenge. Utilization of stem cells, specifically adipocyte-derived mesenchymal stem cells-conditioned medium (ADMSC-CM) and amniotic membrane mesenchymal stem cells-conditioned medium (AMSC-CM), may serve as a novel therapeutic option. This study aims to compare the efficacy of topical ADMSC-CM, topical AMSC-CM, and farmazertin gauze dressing (FGD) only on the healing of CPUL. Methods: In this randomized controlled trial, our study recruited 54 subjects with CPUL. Subjects were randomly assigned to topical ADMSC-CM (n = 16), topical AMSC-CM (n = 22), or FGD (n = 16) applied every three days for up to 8 weeks. Data were analyzed using SPSS version 20 for Windows. Results: Healing percentage increased each week in all groups. Statistic differences between groups (p <0.05) were observed for ulcer mean size and depth reduction from week three onwards. No adverse reactions or complications were reported. At the end of the study, based on clinically improved ulcers, topical ADMSC-CM (100.0%) were superior in improving the healing of CPULs compared to topical AMSC-CM (54.55%) and FGD only (50.0%). Conclusion: ADMSC-CM and AMSC-CM are potential therapeutic agents in the management of CPUL, with ADMSC-CM being superior in overall ulcer improvement.