Background: Single-parenthood is recognised as a risk factor for chronic childhood health conditions due to lower family income, resulting in food insecurity and an increased psychological burden. Governmental social assistance may address the risk by ensuring minimum-income protection and financial healthcare access. However, no study has investigated the association between single-parenthood and health statuses among children in families receiving social assistance benefits. This study aimed to examine the association between single-parent households and children’s health among public assistance recipients in Japan by—for the first time ever—using linkage data of two municipal public assistance databases and medical assistance claim data.Methods: We performed a cross-sectional study. Public assistance for households below poverty line ensures their income security and medical care. We extracted individual factors of children aged 15 years or younger in January 2016 and observed until December 2016. We identified one-year prevalence of childhood diseases by using International Classification of Disease, Tenth Edition (ICD-10) codes.Results: Among the 573 participants, 383 (66.8%) lived in single-parent households. A multivariable Poisson regression showed that single-parenthood is associated with a higher prevalence of asthma (prevalence ratio [PR] = 1.62; 95% confidence interval [CI], 1.16-2.26), allergic rhinitis (PR = 1.41; 95% CI, 1.07-1.86), dermatitis and eczema (PR = 1.81; 95% CI, 1.21-2.70), and dental diseases (PR = 1.79; 95% CI, 1.33-2.42), as compared to other households. No association was found between single-parenthood and acute children’s diseases such as respiratory infections, injuries, and intestinal infections.Conclusions: Living in single-parent households is a risk factor for children’s chronic diseases, despite them receiving public assistance benefits. These results may be explained by the increased psychosocial stress, suggesting that the present public assistance system in Japan should provide additional social support. Ameliorating health conditions of children among single-parent households on public assistance can be achieved by closer monitoring of the community. Further investigations are necessary using more detailed information such as environmental factors, the severity of children’s health conditions, the contents of any received treatments, and broader socioeconomic factors.