The aim of this study was to gain further insights into how the brain distinguishes between meaning and syntax during language comprehension. Participants read and made plausibility judgments on sentences that were plausible, morpho-syntactically anomalous, or pragmatically anomalous. In an event-related potential (ERP) experiment, morphosyntactic and pragmatic violations elicited significant P600 and N400 effects, respectively, replicating previous ERP studies that have established qualitative differences in processing conceptually and syntactic anomalies. Our main focus was a functional magnetic resonance imaging (fMRI) study in which the same subjects read the same sentences presented in the same pseudorandomized sequence while performing the same task as in the ERP experiment. Rapid-presentation event-related fMRI methods allowed us to estimate the hemodynamic response at successive temporal windows as the sentences unfolded word by word, without assumptions about the shape of the underlying response function. Relative to nonviolated sentences, the pragmatic anomalies were associated with an increased hemodynamic response in left temporal and inferior frontal regions and a decreased response in the right medial parietal cortex. Relative to nonviolated sentences, the morphosyntactic anomalies were associated with an increased response in bilateral medial and lateral parietal regions and a decreased response in left temporal and inferior frontal regions. Thus, overlapping neural networks were modulated in opposite directions to the two types of anomaly. These fMRI findings document both qualitative and quantitative differences in how the brain distinguishes between these two types of anomalies. This suggests that morphosyntactic and pragmatic information can be processed in different ways but by the same neural systems.