Background/Objectives: The extensive exposure of physicians to the COVID-19 pandemic has contributed to occupational stress and burnout in their daily lives. This study aimed to explore the lived experiences of intern physicians who experienced burnout during the COVID-19 pandemic and to identify potential solutions to enhance clinical practices in future pandemics. Methods: This study employed a qualitative, phenomenological study utilizing in-depth interviews. The participants were 19 first-year intern physicians from public hospitals in Thailand, selected through a purposeful sampling approach who had experienced burnout. Semi-structured interviews were conducted face-to-face and via online platforms. A thematic narrative analysis approach was used. Results: Phenomenological explorations included two parts: the first explored physicians’ workplace conditions while providing patient care, and the second focused on their proposed solutions for policy changes in clinical practices and hospital management. Four main themes in the first part were derived: (1) emotional suffering and burnout; (2) engaging with a high-intensity workplace; (3) hostile work environments; and (4) deterioration of relationships with staff and colleagues. The second part identified three main themes: (1) changes in policy of clinical practices; (2) effective hospital management; and (3) building interpersonal skills. Conclusions: The COVID-19 pandemic has exacerbated challenges faced by intern physicians, such as high-pressure working conditions, deteriorated relationships with colleagues, and ineffective management, all of which contribute to burnout. These challenges require targeted policy changes in clinical practices, effective hospital management, and building interpersonal skills. Recommendations include improved clinical practices, increased academic support, comprehensive orientation programs, effective communication, teamwork assistance, stress management, and transforming organizational culture to value physicians during internships.