Early work on representational specificity and recent findings on temporomandibular joint (TMJ) movement representation raise doubts that a specific swallow representation does exist. Additionally, during cortical stimulation TMJ movements and swallowing show a high overlap of representational areas in the primary motor cortex. It has thus been hypothesized that they overall might share the same neural structures. To differentiate these two movements, we performed a functional MRI (fMRI) study that enabled a direct comparison of functional representation of both actions in the same subject group. Effort during these tasks was controlled by skin conductance response. When balancing effort, we found a comparable neural representation pattern for both tasks but increased resources necessary to perform swallowing in direct comparison between tasks. For the first time, with the usage of fMRI, we demonstrated a representation in the brainstem for swallowing and occlusion. Increased activation for swallowing was observed in bilateral sensorimotor cortex, bilateral premotor and supplementary motor cortex, motor cingulate, thalamus, cerebellar hemispheres, left pallidum, bilateral pons, and midbrain. Peaks of activation in primary motor cortex between both conditions were about 5 mm adjacent. Brainstem activation was found corresponding to the sensory nucleus of the trigeminal nerve, the solitary nucleus for swallowing, and the trigeminal nucleus for occlusion. Our data suggest that cerebral representation of occlusion and swallowing are spatially widely overlapping, differing predominantly with respect to the quantity of neural resources involved. Both brainstem and primary motor representation differ in location with respect to somatotopy and contribution of cranial nerve nuclei.