Background: Health policies are key social determinants of health, but may cause inequalities if their implementation does not match local needs and if resources are misallocated. This study tests the inverse prevention law on school tobacco policies, assessing inequity in their implementation and identifying contributing factors. Methods: A student survey and a staff survey were conducted in 38 schools across six European cities in 2013 and 2016. We assessed tobacco policy and calculated policy-need ratios to measure how well schools implemented a policy in line with adolescent smoking. Gini coefficients of policy-need ratios were used as an inequity measure. We ran a penalized Lorenz regression to identify factors contributing to inequity and used the Shapley decomposition technique to decompose explained Gini coefficients. Results: Gini coefficients were 8.8% in 2013 and 8.9% in 2016, indicating moderately inequitable implementation of school tobacco policies and limited change over time. Socio-economic characteristics and family/home environment contributed the most to these inequities. Conclusions: In line with the inverse prevention law, stronger tobacco policies are not implemented in schools that most need them, and this persisted between 2013 and 2016. Policy-makers should prioritize equity in health policy implementation and devote more resources to contexts with greater need.