Children growing up in poverty have poorer life prospects and that this is true even for children living in high-income countries. According to the OECD Family Database, in 2014, Japan ranked the 26th out of 37 countries in terms of high relative child poverty. This research project, involving the cooperation of medical institutions nationwide, had the aim to explore income inequality and child rearing environment across Japan. We performed cross-sectional questionnaire studies involving children 0-15 years of age and their caregivers during 2014-2015. Out of the 2,214 respondents, 1,907 (86%) had reliable information on both household income and family structure. Our main findings were that one-fifth of the children lived in relative poverty and only one in ten out of these families received public assistance, about two-thirds of single parents (mostly mothers) lived in poverty. Still, as many as two-fifths of the parents living in poverty assessed their life circumstances as satisfactory. Thus, likely the parent does not recognise that these harsh life circumstances imply that their child's capability is and will be deprived. This can be considered as structural violence and does not comply with the standards of social justice. We argue that when striving to eradicate child poverty, it is important to tackle both limited financial resources and deprived capability. Society as a whole, including the medical institutions and staff, need to stand up for these vulnerable children.