Adolescents’ developing empathy may be associated with the frequency of conflict with parents, as well as the level of agreement between adolescent and parental perceptions of the frequency of such conflicts. This 6-year longitudinal study investigated the link between adolescent empathy development and perceptions of the frequency of parent–child conflict, as reported by 467 adolescents (43 % female, from age 13) and both parents. First, we investigated heterogeneity in empathy development by identifying classes of individuals with similar developmental trajectories. Adolescents were categorized into high-, average-, and low-empathy classes. Initial differences between these classes further increased from age 13 to 16, particularly for cognitive empathy. To assess the association between empathy and the frequency of conflict, we compared these empathy classes in terms of initial levels and over-time changes in the frequency of adolescent- and parent-reported conflict. Compared to the average- and high-empathy classes, the low-empathy class evidenced elevated conflict throughout adolescence. Furthermore, the low- and average-empathy classes demonstrated temporary divergence between adolescent- and parent-reported conflict from early- to mid-adolescence, with adolescents underreporting conflict compared to both parents. Adolescents’ agreement with parents was moderated by empathy class, while parents were always in agreement with one another. This may suggest that these discrepancies are related to distortions in adolescents’ perceptions, as opposed to biased parental reports. These findings highlight the potential importance of early detection and intervention in empathy deficiencies, and suggest that lower adolescent empathy may indicate elevated family conflict, even if a failure to consider parents’ perspective leads adolescents to underreport it.