The anthroposophical philosophy is a holistic educational and lifestyle approach. Limited information exists on the health-promoting behavioral norms and obesity rates among children living anthroposophical vs. conventional lifestyles. This study aims to compare the prevalence of childhood obesity, and parents' perceptions of their children's food environment, between anthroposophical and conventional education systems. We performed a cross-sectional analysis of the National Anthropometric Measurement Survey for first grade students in Israel, comparing anthroposophical schools with matched conventional schools. Additionally, an online survey was distributed among parents of children in both school systems, assessing children's eating norms and dietary intake. Overweight and obesity rates were higher among students in conventional schools (n = 205,500) compared to anthroposophical schools (n = 2247) (11.2% vs. 9.6%, and 7.8% vs. 4.8%, respectively; Pv < 0.001). Anthroposophical schools were perceived by more parents to have health-promoting curricula, health promoting teacher behavior, and health promoting social dietary norms, while their children's dietary intake was perceived as healthier both in school and in the after-school, social, and familial environment (Pv < 0.001). Children in anthroposophical education exhibited lower overweight and obesity rates, and engaged in more health-promoting behaviors. Further research is needed to explore the relationship between the anthroposophical lifestyle and childhood obesity, and to identify effective anthroposophical strategies for health promotion among children.