English Learners (ELs), students from non-English-speaking backgrounds, are a fast-growing, understudied, group of students in the U.S. with unique learning challenges. Cognitive flexibility--the ability to switch between task demands with ease--may be an important factor in learning for ELs as they have to manage learning in their non-dominant language and access knowledge in multiple languages. We used functional MRI to measure cognitive flexibility brain activity in a group of Hispanic middle school ELs (N = 63) and related it to their academic skills. We found that brain engagement during the cognitive flexibility task was related to both out-of-scanner reading and math measures. These relationships were observed across the brain, including in cognitive control, attention, and default mode networks. This work suggests the real-world importance of cognitive flexibility for adolescent ELs, where individual differences in brain engagement were associated with educational outcomes.