The Office of School Health, a joint program of the Departments of Health and Education, administers New York City's (NYC) body mass index (BMI) surveillance system to monitor childhood obesity. We describe the context, importance, and process for creating a multi-agency, school-based BMI surveillance system using BMI collected from annual FITNESSGRAM® physical fitness assessments conducted as part of a larger physical activity and wellness curriculum in NYC public schools. We also summarize our current system and methodology, highlighting the types of data and data sources that comprise the system and partnership between the Departments of Health and Education that enable data sharing. Strategies for addressing threats to data quality, including missing data, biologically implausible values, and imprecise/subjective weight or height equipment are discussed. We also review current and future surveillance data products, and provide recommendations for collecting, analyzing, interpreting, and reporting BMI data for childhood obesity surveillance. Collaboration between Departments of Health and Education as well as attention to safeguards of BMI reporting and data quality threats have enabled NYC to collect high quality BMI data to accurately monitor childhood obesity trends. These findings have implications for youth BMI surveillance systems in the United States and globally., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Authors.)