The aim of this study was to examine the psychometric properties of the Postpartum Bonding Questionnaire (PBQ) in Japanese mothers. Additionally, we investigated the association between postpartum bonding and postnatal depression. The participants of this study were 1786 Japanese mothers, recruited during their infants’ 3 months check-ups at a public health center. The mothers completed the PBQ and the Edinburgh Postnatal Depression Scale (EPDS). We examined the factor structure of the PBQ. However, we were unable to confirm the original 4 factors. A 1-factor solution was extracted by omitting 9 items that did not have significant loadings onto the single factor. According to the cut-off values of the original PBQ, the positive rate was 7.7%. The PBQ score was moderately correlated with the EPDS score. The abridged 16-item Japanese version of the PBQ can be used as a reliable screening tool during check-ups for Japanese mothers. Health practitioners should pay attention to mothers who have bonding disturbances at postpartum.