Drawing upon data gathered from 9301 Year 7 students (12–13 years old) from 46 secondary schools in England, this study represents the first larger‐scale attempt to compare their actual set allocations in maths with the counterfactual position where their allocation to sets is based solely on their prior attainment at the end of primary school [using their Key Stage 2 (KS2) fine‐grained scores in maths]. Through such an analysis, the study found that nearly a third of students (31.2%) had been misallocated to lower or higher sets than their KS2 results would have warranted. Beyond this, school setting practices were found to exacerbate differences in set allocation in relation to gender and ethnicity, but not socioeconomic background. The odds of girls being misallocated to lower sets in maths than their prior attainment would warrant was found to be 1.5 times higher than that for boys. Similarly, the odds of Black students being misallocated to lower sets was 2.4 times higher than for White students, whilst the odds of Asian students being misallocated to lower maths sets was 1.7 times higher than for White students. The article concludes by reflecting on the significant role that setting by attainment in secondary school can play in exacerbating already established patterns of educational inequalities in gender and ethnicity.