Despite its reported effectiveness for the acquisition of motor skills, we know little about how motor imagery (MI)-based brain activation and performance evolves when MI (the imagined performance of a motor task) is used to learn a complex motor skill compared to physical practice (PP). The current study examined changes in MI-related brain activity and performance driven by an equivalent bout of MI- or PP-based training. Participants engaged in 5 days of either MI or PP of a dart-throwing task. Brain activity (via fMRI) and performance-related outcomes were obtained using a pre/post/retention design. Relative to PP, MI-based training did not drive robust changes in brain activation and was inferior for realizing improvements in performance: Greater activation in regions critical to refining the motor program was observed in the PP versus MI group posttraining, and relative to those driven via PP, MI led only to marginal improvements in performance. Findings indicate that the modality of practice (i.e., MI vs. PP) used to learn a complex motor skill manifests as differences in both resultant patterns of brain activity and performance. Ultimately, by directly comparing brain activity and behavioral outcomes after equivalent training through MI versus PP, this work provides unique knowledge regarding the neural mechanisms underlying learning through MI.