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Background: Ring finger protein 213 (RNF213) is a susceptibility gene of moyamoya disease (MMD). A previous case–control study and a family analysis demonstrated a strong association of the East Asian‐specific variant, R4810K (rs112735431), with MMD. Our aim is to uncover evolutionary history of R4810K in East Asian populations. Methods: The RNF213 locus of 24 MMD patients in Japan were sequenced using targeted‐capture sequencing. Based on the sequence data, we conducted population genetic analysis and estimated the age of R4810K using coalescent simulation. Results: The diversity of the RNF213 gene was higher in Africans than non‐Africans, which can be explained by bottleneck effect of the out‐of‐Africa migration. Coalescent simulation showed that the risk variant was born in East Asia 14,500–5100 years ago and came to the Japanese archipelago afterward, probably in the period when the known migration based on archaeological evidences occurred. Conclusions: Although clinical data show that the symptoms varies, all sequences harboring the risk allele are almost identical with a small number of exceptions, suggesting the MMD phenotypes are unaffected by the variants of this gene and rather would be more affected by environmental factors. [ABSTRACT FROM AUTHOR]