A substantial amount of variation in reading comprehension skill is explained by listening comprehension skill, suggesting tight links between printed and spoken discourse processing. In addition, both word level (e.g., vocabulary) and discourse–level sub-skills (e.g., inference-making) support overall comprehension. However, while these contributions to variation in comprehension skill have been well-studied behaviorally, the underlying neurobiological basis of these relationships is less well understood. In order to examine the neural bases of individual differences in reading comprehension as a function of input modality and processing level, we examined functional neural activation to both spoken and printed single words and passages in adolescents with a range of comprehension skill. Data driven Partial Least Squares Correlation (PLSC) analyses revealed that comprehension skill was positively related to activation in a number of regions associated with discourse comprehension and negatively related to activation in regions associated with executive function and memory across processing levels and input modalities.