The principles of school choice and diverse provision underpin transition to secondary education in a majority of countries. This article focuses on the potential for structural diversity to constrain rather than promote choice. Although intended to improve equity in access and quality of provision, choice‐based systems serve to homogenise school intakes and magnify attainment differences between schools. School choice decisions become high‐stakes in such contexts, because eventual school placements influence the future character of children’s schooling. In Northern Ireland, existing community divisions are reflected in the available school types, with a majority of places at either Catholic or de facto Protestant schools, and only a small number at Integrated schools. This results in high levels of homogenisation along community lines. In addition, the provision of separate grammar and non‐grammar schools means that intakes are also academically stratified, resulting in the extreme between‐school attainment differences characteristic of systems arranged in this way. Drawing on documentary evidence and a survey of transition‐age children, this research discusses how school choice within structurally complex systems can be constrained. The main focus is on how children’s education rights, as set down in the United Nations Convention on the Rights of the Child, are placed at risk by the interaction of system‐level divisions. It concludes that school choice arrangements in Northern Ireland do not operate in compliance with children’s education rights when tested against each of the requirements set out in Tomasevski’s 4‐As scheme, namely that education provision must be available, accessible, acceptable and adaptable.