Obesity during development has been reported to be a determinant factor in the future development of non-communicable diseases (NCDs). Parental obesity is suggested to be a predictor of children’s obesity, and it is important to consider parental factors to prevent NCDs in the progeny. Previously, we showed that paternal height had a stronger association with infant birth weight than paternal body mass index (BMI) in the Japanese population. However, only a few studies have examined the association between paternal physique and postnatal obesity. This study aimed to investigate the association between parental physique and obesity in children at the age of 3. This study used fixed data on 33,291 parent–child pairs from the Japan Environment and Children’s Study, an ongoing national birth cohort study. The association between paternal physique (BMI and height) and children’s obesity at the age of 3 was examined using multivariate logistic regression analysis. The higher the paternal BMI quartiles, the higher the odds ratio for obesity in male and female children at 3 years of age (P < 0.0001). However, paternal height quartiles were not associated with male or female obesity. These results differ from the association between paternal physique and infant birth weight, and it is possible that prenatal epigenetic and environmental factors of paternal origin were responsible for the differences between these two studies. The association between paternal BMI and obesity in children at the age of 3 suggests that paternal factors may be involved in the development of NCDs in future progeny.