Project Energize is a through-school nutrition and activity programme that is being evaluated in a 2-year, cluster-randomised, longitudinal study. The present paper describes the background of the programme and study, the programme development and delivery, the study methodology including randomisation, measurement and analysis tools and techniques, and the mix of the study population. The programme is being delivered to sixty-two primary schools with sixty-two control schools, each limb containing about 11 000 students. The children in the evaluation cohort are 5 or 10 years old at enrolment; the randomisation protocol has achieved post-consent enrolment of 3000 evaluation participants, who are comparable by age, sex and school decile. End-point measures include body composition and associated physical characteristics, fitness, home and school environment and practice.