Within pediatric graduate medical education, the care of transgender youth presents opportunities for deepening learners' understanding of equity, access, the role of the physician as an advocate, and health disparities caused by stigma and minority stress. However, when a pediatric resident objects to providing health care to this uniquely vulnerable population owing to their personal beliefs and values, how should pediatrician-educators respond? Important reasons to respect healthcare professionals' conscience have been described in the scholarly literature; however, equally important concerns have also been raised about the extent to which conscientious objection should be permitted in a pluralistic society, particularly given power differentials that favor healthcare professionals and grants them a monopoly over certain services. In the context of medical education, however, residents are in a unique position: they are simultaneously learners and employees, and although privileged relative to their patients, they are also vulnerable in relation to the hierarchy of healthcare and of institutions. We must find a compassionate balance between nurturing the evolving conscience of students and trainees and protecting the health and well-being of our most vulnerable patients. Educators have an obligation to foster empathy, mitigate bias, and mentor their learners, regardless of beliefs, but in some cases, they may recognize that there are limits: patients’ welfare ultimately takes precedence and trainees should be guided toward alternative career paths. We explore the limits of conscientious objection in medical training and propose a framework for pediatrician-educators to support learners and patients in challenging circumstances.