Mental health assessments of both members of a couple are important when considering the child-rearing environment. The prevalence and factors associated with both parents' psychological distress have not been fully investigated. A nationally representative sample from the 2016 Comprehensive Survey of Living Conditions in Japan was used to examine the prevalence of moderate and severe psychological distress in parents in the first year after childbirth. In total, 3,514 two-parent households raising children under one year old met the study criteria. The Japanese version of Kessler 6 was used to assess moderate and severe psychological distress. The prevalence of either or both parents experiencing psychological distress in the first year after birth were 15.1% and 3.4%, respectively. A multivariate logistic regression analysis showed factors of fathers who worked ≥ 55 h a week, reduced duration of sleep in mothers, age in months of the youngest child, and high household expenditures were significantly associated with both parents simultaneously having moderate or severe psychological distress. This study implied the importance of prevention and early detection of parental psychological distress in both parents. Assessing parents' psychological distress and work-style reform in the childcare period is an urgent issue to improve their mental health conditions.