The Edinburgh Postnatal Depression Scale (EPDS) is a widely used screening tool for perinatal depression. Its factor structure is still a debatable topic. Our study aimed to examine the factor structure and measurement invariances of the Japanese version of the EPDS from late pregnancy to early postpartum. A total of 633 women were followed with the EPDS at three times over the perinatal period: late pregnancy (n= 633), 5 days after childbirth (n= 445), and 1 month after childbirth (n= 392). We randomly divided the participants into two groups: one for exploratory factor analyses (EFAs) and another for confirmatory factor analyses (CFAs). The result of the EFAs indicated different factor models at each time point. Hence, CFAs were performed using the second sample set to compare different models including the ones previously reported. A 3-factor model consisting of depression (items 7, 9), anxiety (items 4, 5), and anhedonia (items 1, 2) (Kubota et al., 2018) was consistently stable during the whole perinatal period. Kubota’s 3-factor model showed invariance across the perinatal period.