This study aimed to analyze the phenomenon of conflict in physical education classes. It was conducted as an applied study using a qualitative approach and the reflexive thematic analysis method proposed by Braun and Clarke (2019). Purposive sampling was employed, involving 16 participants—including teachers, lead teachers, physical education curriculum specialists, and professors in the fields of educational sciences and psychology. Data were collected through in-depth, semi-structured interviews, and the validity of the findings was ensured through triangulation of sources and coders, as well as participant and critical friend reviews. The analysis yielded three main themes derived from 128 concepts and 14 sub-themes: 1) Causes of conflict, categorized into contextual/environmental factors, student-related factors, factors related to the nature of the subject, and teacher behavior (63 concepts); 2) Forms of conflict, identified as active cooperation, passive compliance, avoidance, and direct confrontation (27 concepts); and 3) Strategies, categorized into teacher teaching-learning strategies, suitable environmental settings, interactive and dialogue-based strategies, teacher empowerment, teaching social-emotional skills to students, and teacher management skills (38 concepts). Conflict in physical education classes is a multi-level phenomenon, a significant portion of which manifests covertly; its effective management requires the simultaneous empowerment of teachers and structural reforms regarding class density, facilities, equipment, and the institutional status of the subject.