Despite the increasing trend of paternal engagement in caregiving, fathers remain underrepresented in studies on parenting and childhood obesity. This study examined the association between father involvement in caregiving and child's weight status within a longitudinal dataset from Japan. The data were obtained from a population-based cohort study in Japan (N = 29 584). The association between father's involvement in child caregiving (age 18 months) on the weight status of the same children at age 3.5 years was examined by logistic regression and linear regression analysis. Furthermore, we checked the interaction between maternal employment & father involvement by creating four mutually exclusive groups of families. Children whose fathers were highly involved in caregiving were less likely to be overweight (OR = 0.90, 95% CI, 0.85-0.96). Employed mothers with high paternal involvement in caregiving were 30% less likely to have children with overweight or obesity compared to those with low paternal involvement (95% CI, 0.55-0.90). Father involvement in caregiving is associated with the development of overweight or obesity in early childhood, and may also modify the association between maternal employment and child's weight status. Social policies to support shared child-rearing such as expanding paid parental leave could help families to raise children with healthy weight.