Empathy plays a key role in maintaining close relationships and promoting prosocial conflict resolution. However, research has not addressed the potential emotional cost of adolescents’ high empathy, particularly when relationships are characterized by more frequent conflict. The present 6-year longitudinal study (N = 467) investigated whether conflict with parents predicted emotion dysregulation more strongly for high-empathy adolescents than for lower-empathy adolescents. Emotion dysregulation was operationalized at both the experiential level, using mood diary data collected for 3 weeks each year, and at the dispositional level, using annual self-report measures. In line with predictions, we found that more frequent adolescent–parent conflict predicted greater day-to-day mood variability and dispositional difficulties in emotion regulation for high-empathy adolescents, but not for average- and low-empathy adolescents. Mood variability and difficulties in emotion regulation, in turn, also predicted increased conflict with parents. These links were not moderated by empathy. Moreover, our research allowed for a novel investigation of the interplay between experiential and dispositional emotion dysregulation. Day-to-day mood variability predicted increasing dispositional difficulties in emotion regulation over time, which suggests that experiential dysregulation becomes consolidated into dispositional difficulties in emotion regulation. Moderated mediation analyses revealed that, for high-empathy adolescents, conflict was a driver of this dysregulation consolidation process. Finally, emotion dysregulation played a role in overtime conflict maintenance for high-empathy adolescents. This suggests that, through emotion dysregulation, high empathy may paradoxically also contribute to maintaining negative adolescent–parent interactions. Our research indicates that high empathy comes at a cost when adolescent–parent relationships are characterized by greater negativity.