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Academic physicians must teach elements in an Accreditation Council for Graduate Medical Education (ACGME)-mandated curriculum while balancing career development and clinical workload. Exploring educator perceptions on the learning environment and comparing two instructional methods (traditional didactics [TD] vs. flipped classroom [FC]) in one pediatric subspecialty may elucidate current challenges, barriers, and strategies to optimize learning and educator satisfaction. A randomized trial comparing effectiveness and learner preference for FC versus TD physiology teaching was conducted in ACGME-accredited neonatal-perinatal medicine (NPM) fellowship programs in 2018 to 2019. Educator preferences were elicited through online surveys pre- and postintervention. Free-text comments were provided for questions exploring strengths, challenges, and opportunities in fellowship education. Statistical analysis included comparisons of demographics and pre-post-intervention educator responses between groups. Thematic analysis of text responses was conducted to identify common subthemes. From 61 participating programs, 114 FC educators and 130 TD educators completed surveys. At baseline, all educators experienced professional satisfaction from teaching fellows, but noted challenges with time available to create and/or deliver educational content, limited content expertise amongst faculty, colleagues' limited enthusiasm toward educating fellows, and lack of perceived value of education by institutions given limited protected time or credit toward promotion. Postintervention, educators in both groups noted a preference to teach physiology using FC due to interactivity, learner enthusiasm, and learner-centeredness. FC educators had a 17% increase in preference to teach using FC ( Overall, NPM educators in a trial evaluating a standardized, peer-reviewed curriculum report professional satisfaction from teaching, but described logistical challenges with developing/delivering content. Educators preferred instruction using FC, but identified challenges with learner preparedness and ensuring adequate educator time and skill. Future efforts should be dedicated to addressing these barriers.· Many challenges exist for educators teaching neonatal-perinatal medicine fellows, including time, support, and recognition.. · Many educators preferred using flipped classroom methodology with a standardized curriculum due to interactivity and learner-centeredness.. · Benefits of a standardized, peer-reviewed curriculum include reduced preparation time, adaptability of content, and learning environment enhancement..