Although cognitive behavioral therapy (CBT) is effective for childhood anxiety disorders, approximately 40% of youth remain anxious after treatment. Metacognitive therapy (MCT-c) for children with generalized anxiety disorder (GAD) has shown promising effects. The present study aimed to examine if CBT and MCT-c show differential effects in children with primary GAD based on baseline characteristics, in a quasi-experimental design. To investigate which treatment is most beneficial for whom, three potential moderators: age, symptom severity, and comorbid social anxiety were examined. Sixty-three children aged 7–14 completed CBT or MCT-c. Participants were assessed before and after treatment. Both CBT and MCT-c were highly effective in treatment of childhood GAD. None of the selected variables significantly moderated treatment outcomes. Subgroups of children with high symptom severity and social anxiety comorbidity showed trends of responding better to CBT. Methodologically stronger studies are needed to facilitate a better adaptation of treatment for children with GAD.