Background: The current nonrandomized clinical trial explored changes over time in children with an anxiety disorder during stepped care, manual-based cognitive behaviour therapy (CBT). Methods: Clinically anxious children (8–12 years, n = 133) and their parents participated in child focused CBT (10 sessions). If assessments indicated additional treatment was necessary, participants could step up to a second and possibly third treatment phase (each 5 sessions) including more parental involvement. Results: After the first treatment phase 45% of the Intention-To-Treat sample was free of any anxiety disorder; after the second and third phase an additional 17% and 11% respectively. In total, 74% of the children no longer met criteria for any anxiety disorder following treatment. Child and parent reported anxiety and depression symptoms of children improved significantly during all treatment phases, as well as child reported anxiety sensitivity and negative affect. Children participating in more treatment showed significant improvements during additional treatment phases, indicating that late change occurred for the subgroup that had not changed during the first phase. Conclusions: Stepped care offers a standardized, assessment based, yet tailored treatment approach for children with anxiety disorders. A more intensive treatment is offered when initial CBT is insufficient, providing children additional opportunities to reach the desired outcome.