Schools are common sites for obesity prevention interventions. Although many theories suggest that the school context influences weight status, there has been little empirical research. The objective of this study was to explore whether features of the school context were consistently and meaningfully associated with pupil weight status (overweight or obese). Exploratory factor analysis of routinely collected data on 319 primary schools in Devon, England, was used to identify possible school-based contextual factors. Repeated cross-sectional multilevel analysis of five years (2006/07-2010/11) of data from the National Child Measurement Programme was then used to test for consistent and meaningful associations. Four school-based contextual factors were derived which ranked schools according to deprivation, location, resource and prioritisation of physical activity. None of which were meaningfully and consistently associated with pupil weight status, across the five years. The lack of consistent associations between the factors and pupil weight status suggests that the school context is not inherently obesogenic. In contrast, incorporating findings from education research indicates that schools may be equalising weight status, and obesity prevention research, policy and practice might need to address what is happening outside schools and particularly during the school holidays.