After-Action Reports (AARs) are retrospective summaries that capture key information and lessons learned from emergency response exercises and real incidents. The AAR is a commonly used evaluation tool used by the Centers for Disease Control and Prevention as part of the Public Health Emergency Preparedness (PHEP) program. It is used as a metric of accountability and awardee performance. The objectives of this study were to qualitatively analyze AARs of public health preparedness programs and develop a coding scheme for standardizing future review and analysis of AARs. We evaluated 14 AARs (4 exercises and 10 real incidents) generated between 2012 and 2018. We applied inductive qualitative analyses using ATLAS.Ti software. While, previous exercises focused on medical countermeasure responses, real-world incidents focused on natural disasters and infectious disease outbreaks. Six overarching themes emerged: Communications, Coordination, Resource Distribution, Unified Planning, Surveillance, and Knowledge Sharing. A standardized analysis format is proposed for future use.