Objective To provide evidence of the association between CLTA-4 gene polymorphisms and alopecia areata (AA). Methods PubMed, EMBASE, Web of Science, Cochrane, Wanfang, and CNKI databases were searched until 30 April 2021. The selection was completed according to the inclusion and exclusion criteria. The study quality assessment was based on Newcastle-Ottawa Scale. The assessment of the association was measured by ORs and 95%CIs. Results Nine studies, containing 2858 AA cases and 5444 disease-free control subjects were included. For rs231775 polymorphism, no significant association with AA was found, which was A vs. a, OR = 1.02 [0.81, 1.30], p = 0.85; AA vs. aa, OR = 1.26 [0.81, 1.97], p = 0.31; Aa vs. aa, OR = 1.04 [0.54, 2.01], p = 0.91; AA + Aa vs. aa, OR = 1.04 [0.71, 1.53], p = 0.82; AA vs. Aa + aa, OR = 1.31 [0.97, 1.78], p = 0.08. For rs3087243 polymorphism, also no significant association was found, which was A vs. a, OR = 0.93 [0.78, 1.11]; p = 0.40, AA vs. aa, OR = 0.68 [0.44, 1.06]; p = 0.09; Aa vs. aa, OR = 0.87 [0.45, 1.68], p = 0.68; AA + Aa vs. aa, OR = 0.93 [0.68, 1.28], p = 0.66; AA vs. Aa + aa, OR = 0.78 [0.34, 1.81], p = 0.57. For rs231726 polymorphism, a significant correlation was found, which was A vs. a, OR = 0.76 [0.70, 0.82], p < 0.05. Conclusions A significant correlation between CTLA-4 rs231726 polymorphism and AA susceptibility was found, but no significant association of CTLA-4 gene rs231775 and rs3087243 polymorphisms and AA susceptibility was found.