This paper studies whether pupil performance gains achieved by autonomous schools -specifically academy schools in England -can be attributed to the strategic exclusion of poorly performing pupils. In England there have been two phases of academy school introduction, the first in the 2000s being a school improvement programme for schools serving disadvantaged pupil populations, the second a mass academisation programme in the 2010s which by contrast enabled better performing schools to become academies. Overall, on average across both programmes, exclusion rates are higher in academy schools. When the two programmes are considered separately, the earlier programme featured a much higher increase in the incidence of permanent exclusion. However, a number of simulated counterfactual experiments based on the statistical estimates show that rather than being used as a strategic means of manipulation to boost measured school performance, the higher rate of exclusion is instead a feature of the rigorously enforced discipline procedures that the pre-2010 academies adopted.