This paper investigates the relationship between music qualification choice and academic performance in secondary education in England at Key Stage 4 (KS4; usually at ages 15 and 16). We analysed data from 2257 pupils at 18 educational settings in a city in the southeast of England. Two regression analyses with clustered errors modelled KS4 music qualification choice and GCSE academic achievement in English, Mathematics and other English Baccalaureate subjects, while controlling for a range of demographic, academic and socio-economic variables. Choice of music as a subject at KS4 was positively associated with the total volume of KS4 qualifications entered for examination and was also predicted by coming from an affluent neighbourhood. Furthermore, this choice of music at KS4 was associated with greater academic performance on English Baccalaureate subjects above and beyond other significant predictors (gender, language, prior academic achievement, total volume of KS4 qualifications and neighbourhood socio-economic status; local Cohen's f-squared = 0.09). These results point to moderate but significant additive effect of studying music at KS4 in relation to performance on core GCSE subjects. We also found that schools with KS4 music qualification choice greater than the national average were higher in overall academic attainment, in the proportion of pupils attending extra-curricular instrumental lessons, and in our composite measure of school's engagement with a local music education hub. The results are interpreted in light of sociological theories of education in an attempt to better understand the underlying systemic factors affecting youth music engagement.