This paper examines the influence of single parenthood on children's academic achievement in Japan. While some studies have examined the academic achievement gap associated with family structure, a limitation of existing research is the focus on differences between the mean levels of academic achievement of children in single-parent and two-parent families. Using data from the Programme for International Student Assessment (PISA) conducted by the Organisation for Economic Co-operation and Development (OECD) in 2012, this paper investigates the effects of single parenthood across the entire distribution of children's academic achievement by using quantile regression techniques. The results of quantile regression analyses indicated that the magnitude of the academic achievement gap between children in single-parent and two-parent families was not equal for each quantile of the conditional distribution of children's academic achievement. The negative effect of single motherhood on children's academic achievement was more profound at lower quantiles, whereas the negative effect of single fatherhood was more profound at the median level. Furthermore, the extent to which parents' education levels accounted for the negative effects of single parenthood was not equal for each quantile of the conditional distribution of children's academic achievement. The effects of single parenthood at lower quantiles were not well explained by parents' education levels, and this tendency was especially obvious in the academic achievement of children in single-father families. This result suggests that low academic achievement of children in single-mother families may be caused by the mothers' low education levels and accompanying low income, whereas poor academic achievement of children in single-father families is likely to be mainly due to the absence of mothers rather than the fathers' low education levels. Based on the empirical evidence obtained in this paper, policy implications regarding the significance and limitations of economic support for single-parent families in terms of reducing educational inequality are discussed.