Spatial reasoning is a critical skill in many everyday tasks and in science, technology, engineering, and mathematics disciplines. The current study examined how training on mental rotation (a spatial reasoning task) impacts the completeness of an encoded representation and the ability to rotate the representation. We used a multisession, multimethod design with an active control group to determine how mental rotation ability impacts performance for a trained stimulus category and an untrained stimulus category. Participants in the experimental group (n = 18) showed greater improvement than the active control group (n = 18) on the mental rotation tasks. The number of saccades between objects decreased and saccade amplitude increased after training, suggesting that participants in the experimental group encoded more of the object and possibly had more complete mental representations after training. Functional magnetic resonance imaging data revealed distinct neural activation associated with mental rotation, notably in the right motor cortex and right lateral occipital cortex. These brain areas are often associated with rotation and encoding complete representations, respectively. Furthermore, logistic regression revealed that activation in these brain regions during the post-training scan significantly predicted training group assignment. Overall, the current study suggests that effective mental rotation training protocols should aim to improve the encoding and manipulation of mental representations.