<p>Parent-child behavioral synchrony—the dyad’s moment-to-moment coordination of behavior and emotion—supports children’s socioemotional development, yet most evidence comes from cross-sectional community samples using global indices, limiting clinical insight for heterogeneous conduct problems (CP). This prospective study tested baseline differences and treatment-related change in discrete synchrony facets among clinic-referred children with CP, comparing CP-only, primary callous-unemotional (CU; CU without internalizing problems), and secondary CU (CU with internalizing problems) variants. Mother-child and father-child dyads of <i>N</i> = 234 children aged 2–7 years (74% boys) completed standardized play tasks that were coded into four Mutually Responsive Orientation dimensions (Coordinated Routines, Mutual Cooperation, Harmonious Communication, Emotional Ambience); parents completed questionnaires assessing child CP, CU traits, and internalizing symptoms. A subsample (<i>n</i> = 142) received parent training and was re-assessed post-treatment and at three-month follow-up. At baseline, mother-child Harmonious Communication and Emotional Ambience were significantly lower in secondary CU than in primary CU and CP-only groups. Parent training significantly improved synchrony across dyads from baseline to post-treatment, with maintenance for mothers. However, despite overall gains, synchrony remained lower for secondary CU than primary CU variants at follow-up (mothers), and father-child Harmonious Communication deteriorated from post-treatment to follow-up in secondary CU relative to improvement in primary CU. Findings indicate variant-specific synchrony deficits, especially affective facets, in secondary CU and attenuated normalization following parent training, refining etiological accounts and highlighting the need to tailor synchrony-focused treatment targets for CP subgroups.</p>