Therapeutic alliance and decreases in negative cognitions may play an important role in the outcomes of child trauma-focused cognitive behavioral therapy. However, understanding alliance from multiple perspectives (i.e., therapist, parent, and child) and if changes in negative cognitions differ by type of delivery is limited. The current study examined therapist, parent and child therapeutic alliance and child negative cognition changes over time and as potential mediators of outcomes between Step One, a parent-led therapist-assisted cognitive behavioral therapy (CBT), and therapist-led Trauma-Focused CBT (TF-CBT).Therapist, parent and child therapeutic alliance, child negative cognitions, child posttraumatic stress symptoms (PTSS) and impairment were assessed at the first session, mid-treatment and near the end of treatment among child-parent dyads in Step One (n = 43) and TF-CBT (n = 71). Child PTSS and impairment were also assessed at post-treatment. The rate of change in therapist and parent therapeutic alliance within Step One and TF-CBT did not significantly differ. Changes over time in child alliance ratings differed with a convex curve for Step One and a concave curve for TF-CBT children. Similar decreases in negative cognitions in Step One and TF-CBT children occurred. Neither therapeutic alliance (therapist, parent, and child) nor negative cognitions were mediators of PTSS and impairment outcomes. Therapist therapeutic alliance over time, across treatments was a predictor of child PTSS. Change rates in child therapeutic alliance differs with a parent-led therapist-assisted treatment versus TF-CBT. Therapist alliance may influence child PTSS outcomes in a parent-led and therapist-led CBT treatment.