Background: Anxiety in children is common and incapacitating and increases the risk of mental health disorders in adulthood. Although effective interventions are available, few children are identified and referred for specialist treatment. Alternative approaches in which prevention programmes are delivered in school appear promising. However, comparatively little is known about the best intervention leader (health care-led vs. school-led), long-term effects or the primary preventive value of such programmes.Methods/Design: Preventing Anxiety in Children through Education in Schools, or PACES, is a pragmatic cluster randomised controlled trial evaluating the effectiveness of a cognitive-behavioural therapy prevention programme (FRIENDS) on symptoms of anxiety and low mood in 9- to 10-year-old children. Forty-one schools were randomly assigned to one of three conditions: school-led FRIENDS, health care-led FRIENDS or treatment as usual. Assessments were undertaken at baseline, 6 months and 12 months, with the primary outcome measure being the Revised Child Anxiety and Depression Scale score at 12 months. Secondary outcome measures are changes in self-esteem, worries, bullying and life satisfaction.Discussion: This protocol summarises the procedure for the 24-month follow-up of this cohort. The study will determine the medium-term effectiveness of an anxiety prevention programme delivered in schools.Trial registration: ISRCTN23563048.