Despite major advances in measuring human brain activity during and after educational experiences, it is unclear how learners internalize new content, especially in real-life and online settings. In this work, we introduce a neural approach to predicting and assessing learning outcomes in a real-life setting. Our approach hinges on the idea that successful learning involves forming the right set of neural representations, which are captured in canonical activity patterns shared across individuals. Specifically, we hypothesized that learning is mirrored in neural alignment: the degree to which an individual learner’s neural representations match those of experts, as well as those of other learners. We tested this hypothesis in a longitudinal functional MRI study that regularly scanned college students enrolled in an introduction to computer science course. We additionally scanned graduate student experts in computer science. We show that alignment among students successfully predicts overall performance in a final exam. Furthermore, within individual students, we find better learning outcomes for concepts that evoke better alignment with experts and with other students, revealing neural patterns associated with specific learned concepts in individuals.