To control the spread of COVID-19, the national government of Japan abruptly started the closure of elementary schools on March 2, 2020, but preschools were exempted from this nationwide school closure. Taking advantage of this natural experiment, we examined how the proactive closure of elementary schools affected various outcomes related to children and family well-being. To identify the causal effects of the school closure, we exploited the discontinuity in the probability of going to school at a certain threshold of age in months and conducted fuzzy regression discontinuity analyses. The data are from a large-scale online survey of mothers whose firstborn children were aged 4 to 10 years. The results revealed a large increase in children’s weight and in mothers’ anxiety over how to raise their children. On the outcomes related to marital relationships, such as the incidence of domestic violence and the quality of marriage, we did not find statistically significant changes. These findings together suggest that school closures could have large unintended detrimental effects on non-academic outcomes among children.