Project Energize, a region-wide whole-school nutrition and physical activity programme, commenced as a randomised controlled trial (RCT) in the period 2004–6 in 124 schools in Waikato, New Zealand. In 2007, sixty-two control schools were engaged in the programme, and by 2011, all but two of the 235 schools in the region were engaged. Energizers (trained nutrition and physical activity specialists) work with eight to twelve schools each to achieve the goals of the programme, which are based on healthier eating and enhanced physical activity. In 2011, indices of obesity and physical fitness of 2474 younger (7·58 (sd 0·57) years) and 2330 older (10·30 (sd 0·51) years) children attending 193 of the 235 primary schools were compared with historical measurements. After adjusting for age, sex, ethnicity, socio-economic status (SES) and school cluster effects, the combined prevalence of obesity and overweight among younger and older children in 2011 was lower by 31 and 15 %, respectively, than that among ‘unEnergized’ children in the 2004 to 2006 RCT. Similarly, BMI was lower by 3·0 % (95 % CI − 5·8, − 1·3) and 2·4 % (95 % CI − 4·3, − 0·5). Physical fitness (time taken to complete a 550 m run) was significantly higher in the Energized children (13·7 and 11·3 %, respectively) than in a group of similarly aged children from another region. These effects were observed for boys and girls, both indigenous Māori and non-Māori children, and across SES. The long-term regional commitment to the Energize programme in schools may potentially lead to a secular reduction in the prevalence of overweight and obesity and gains in physical fitness, which may reduce the risk of developing obesity and type 2 diabetes.