Background: Emotional problems such as anxiety and low mood in children are common, impair everyday functioning and increase the risk of severe mental health disorders in adulthood. Relatively few children with emotional health problems are identified and referred for treatment indicating the need to investigate preventive approaches. Methods/Design: The study is designed to be a pragmatic cluster randomized controlled trial evaluating the effectiveness of an efficacious school-based cognitive behavior therapy (CBT) prevention program (FRIENDS) on symptoms of anxiety and low mood in children 9 to 10 years of age. The unit of allocation is schools which are assigned to one of three conditions: school-led FRIENDS, health-led FRIENDS or treatment as usual. Assessments will be undertaken at baseline, 6 months and 12 months. The primary outcome measure is change on the Revised Child Anxiety and Depression Scale. Secondary outcome measures assess changes in self-esteem, worries, bullying and life satisfaction. An economic evaluation will be undertaken. Discussion: As of September 2011, 41 schools have been recruited and randomized. Final 12-month assessments are scheduled to be completed by May 2013.