In humans, the nature of sensory input influences body-related mental processing. For instance, behavioral differences (e.g., response time) can be found between mental spatial transformations (e.g., mental rotation) of viewed and touched body parts. It can thus be hypothesized that distinct brain activation patterns are associated with such sensory-dependent body-related mental processing. However, direct evidence that the neural correlates of body-related mental processing can be modulated by the nature of the sensory stimuli is still missing. We thus analyzed event-related functional magnetic resonance imaging (fMRI) data from thirty-one healthy participants performing mental rotation of visually- (images) and haptically-presented (plastic) hands. We also dissociated the neural activity related to rotation or task-related performance using models that either regressed out or included the variance associated with response time. Haptically-mediated mental rotation recruited mostly the sensorimotor brain network. Visually-mediated mental rotation led to parieto-occipital activations. In addition, faster mental rotation was associated with sensorimotor activity, while slower mental rotation was associated with parieto-occipital activations. The fMRI results indicated that changing the type of sensory inputs modulates the neural correlates of body-related mental processing. These findings suggest that distinct sensorimotor brain dynamics can be exploited to execute similar tasks depending on the available sensory input. The present study can contribute to a better evaluation of body-related mental processing in experimental and clinical settings.