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Abstract Background Pediatric asthma is currently the most prevalent chronic disease in the United States, with children in lower income families disproportionately affected. This increased health burden is partly due to lower-quality and insufficient maintenance of affordable housing. A movement towards ‘green’ retrofits that improve energy efficiency and increase ventilation in existing affordable housing offers an opportunity to provide cost-effective interventions that can address these health disparities. Methods We combine indoor air quality modeling with a previously developed discrete event model for pediatric asthma exacerbation to simulate the effects of different types of energy retrofits implemented at an affordable housing site in Boston, MA. Results Simulation results show that retrofits lead to overall better health outcomes and healthcare cost savings if reduced air exchange due to energy-saving air tightening is compensated by mechanical ventilation. Especially when exposed to indoor tobacco smoke and intensive gas-stove cooking such retrofit would lead to an average annual cost saving of over USD 200, while without mechanical ventilation the same children would have experienced an increase of almost USD 200/year in health care utilization cost. Conclusion The combination of indoor air quality modeling and discrete event modeling applied in this paper can allow for the inclusion of health impacts in cost-benefit analyses of proposed affordable housing energy retrofits.