Vitiligo is a common skin disease for which immunomodulating calcineurin inhibitors have been considered reasonable treatment. We searched the MEDLINE, Embase, and Cochrane central register of controlled trials databases for articles published prior to September 2014. Thirteen studies were included in the meta-analysis. After pooling the trials, we concluded that calcineurin inhibitors showed a better therapeutic effect on vitiligo than placebo, according to lesion report (RR = 2.62, 95%CI, 1.39-4.93, p = 0.003) and patient report (RR = 1.42, 95%, 0.87-2.31, p = 0.157). Subgroup analysis was performed to determine whether the combination with phototherapy was a source of heterogeneity. The trial sequence analysis indicated that the results of combined therapy by lesion report were reliable and conclusive. However, in the patient report trials, the frequency of lesions on the hand and foot was higher, and the effect of combined therapy was still not significant. Calcineurin inhibitors showed a better therapeutic effect than placebo in the treatment of vitiligo with phototherapy. However, the typical UV-resistant sites (i.e., hand and foot) were still difficult to cure even with combined therapy. Because of concerns about photocarcinogenesis, the clinical application of combined therapy should be explored with caution.