Concerns have been raised in numerous countries over declining rates of active transport to school. In a UK context, the pupil-school commute is estimated to contribute around 658 kilotonnes of CO2 per year; however, tackling this issue effectively requires an improved understanding of how emissions can be modelled and mapped over a variety of scales. This paper implements a new estimation technique for the modelling of CO2 emissions linked with the school commute that integrates both transport network-level routing and geographically disaggregate vehicle emissions data. The model is then applied to a national cohort of pupils in England. Areas demonstrating the highest emissions were typically more rural and/or comprising more affluent resident populations. Emissions were also shown to increase with school year, with larger step changes between educational stages reflecting the different geography of school locations. Furthermore, where secondary school entry policies were selective or based on a religious domination, average emissions were typically higher than in non-selective schools.