Background: Burnout is common among physicians who care for critically ill patients and is known to contribute to worse patient outcomes. Fellows training in pulmonary and critical care medicine (PCCM) have risk factors that make them susceptible to burnout; for example, clinical environments that require increased intellectual and emotional demands with long hours. The Accreditation Council for Graduate Medical Education has recognized the increasing importance of trainee burnout and encourages training programs to address burnout. Objective: To assess factors related to training and practice that posed a threat to the well-being among fellows training in PCCM and to obtain suggestions regarding how programs can improve fellow well-being. Methods: We conducted a qualitative content analysis of data collected from a prior cross-sectional electronic survey with free-response questions of fellows enrolled in pulmonary, PCCM, and critical care medicine training programs in the United States. Fellows were asked what factors posed a threat to their well-being and what changes their training program could implement. Responses were qualitatively coded and categorized into themes using thematic analysis. Results: A total of 427 fellows (44% of survey respondents) completed at least one free-response question. The majority of respondents (60%) identified as male and white/non-Hispanic (59%). The threats to well-being and burnout were grouped into five themes: clinical burden, individual factors, team culture, limited autonomy, and program resources. Clinical burden was the most common threat discussed by fellows. Fellows highlighted factors contributing to burnout that specifically pertained to trainees including challenging interpersonal relationships with attending physicians and limited protected educational time. Fellows proposed solutions addressing clinical care, changes at the program or institution level, and organizational culture changes to improve well-being. Conclusion: This study provides insight into factors fellows report as contributors to burnout and decreased well-being in addition to investigating fellow-driven solutions toward improving well-being. These solutions may help pulmonary, PCCM, and critical care medicine program directors better address fellow well-being in the future.