Background Vitiligo manifests as hypo-to de-pigmented macules, which are sometimes associated with leukotrichia. For complete cosmetic improvement, the repigmentation of leukotrichia is an important component. Methods This randomized controlled trial included patients with stable vitiligo with leukotrichia. Two vitiligo patches in each patient were randomized to receive either of the two procedures. The patients were followed up for 9 months posttransplantation. The efficacy of hair follicle cell suspension (HFCS) with epidermal cell suspension (ECS) in repigmentation of leukotrichia and skin in vitiligo was compared. Results A total of 20 patients underwent the procedure, and 19 completed the follow-up. The area of the vitiligo patch and the number of leukotrichia in the patches were comparable between the two groups. There was a significant difference in the mean AE S.D. number of cells transplanted between the two groups (5.06 9 10 5 in HFCS vs. 39.8 9 10 5 in ECS, P < 0.0001). The percentage viability of cells and proportion of melanocytes were comparable between the two groups. A total of 10 patients in HFCS and eight patients in ECS had repigmentation of leukotrichia. The mean AE S.D. percentages of depigmented hair showing repigmentation at nine months were 7.42 AE 11.62% in HFCS and 11.42 AE 17.90% in ECS (P = 0.4195), whereas the mean AE S.D. percentage repigmentation of vitiligo patches was 61.58 AE 42.68% in HFCS and 78.68 AE 30.03% in ECS (P = 0.1618). Conclusions The mean number of cells transplanted in the HFCS group was about eight times less than those in ECS. ECS was better than HFCS in repigmentation of leukotrichia and vitiligo, although the difference was not statistically significant.