Facial muscles drive whisker movements, which are important for active tactile sensory perception in mice and rats. These whisker muscles are innervated by cholinergic motor neurons located in the lateral facial nucleus. The whisker motor neurons receive synaptic inputs from premotor neurons, which are located within the brain stem, the midbrain, and the neocortex. Complex, distributed neural circuits therefore regulate whisker movement during behavior. This review focuses specifically on cortical whisker motor control. The whisker primary motor cortex (M1) strongly innervates brain stem reticular nuclei containing whisker premotor neurons, which might form a central pattern generator for rhythmic whisker protraction. In a parallel analogous pathway, the whisker primary somatosensory cortex (S1) strongly projects to the brain stem spinal trigeminal interpolaris nucleus, which contains whisker premotor neurons innervating muscles for whisker retraction. These anatomical pathways may play important functional roles, since stimulation of M1 drives exploratory rhythmic whisking, whereas stimulation of S1 drives whisker retraction.