Executive functions (EFs) are predictive of early academic attainment. However, there is little research investigating whether academic outcomes are differentially associated with cognitive abilities during adolescence, when EFs are still developing. Using a large population-based sample, three latent components, working memory, inhibitory control, and processing speed, were characterised from ten cognitive tasks. These components were used in structural equation models alongside measures of IQ (vocabulary, matrix reasoning) to assess specific relationships with English, maths and science attainment at 16 years of age while controlling for socio-economic status (SES) and previous attainment at age 11. Cognitive measures and SES contributed to individual differences in change in academic performance across adolescence, and specific associations between cognitive abilities and academic subjects could be observed. These results show that SES and cognitive abilities, in particular working memory, continue to influence academic progress beyond childhood, and that these associations are specific to individual academic subjects.