Abnormalities in MYO5B, which encodes an unconventional myosin Vb, not only cause microvillus inclusion disease but also cholestatic liver disease, including benign recurrent intrahepatic cholestasis (BRIC). However, MYO5B-related cholestasis has not yet been reported in Japan. In this study, we present the case of a female patient in her thirties, who had developed jaundice, without diarrhea, in the first year after birth. The jaundice spontaneously subsided and occasionally recurred. Whole-exome sequencing identified two pathogenic variants in MYO5B: a nonsense mutation (c. G1124A: p. W375X) and a missense mutation (c.C2470T: p.R824C). Therefore, the patient was diagnosed with MYO5B-associated BRIC. This is the first reported case of cholestasis with a defined MYO5B defect in Japan.