The central nervous system both influences and is influenced by the gastrointestinal system. Most research on this gut-brain connection has focused on how ascending signals from the gut and its microbiome alter brain function. Less attention has focused on how descending signals from the central nervous system alter gut function. Here, we used retrograde transneuronal transport of rabies virus to identify the cortical areas that most directly influence parasympathetic and sympathetic control of the rat stomach. Cortical neurons that influence parasympathetic output to the stomach originated from the rostral insula and portions of medial prefrontal cortex, regions that are associated with interoception and emotional control. In contrast, cortical neurons that influence sympathetic output to the stomach originated overwhelmingly from the primary motor cortex, primary somatosensory cortex, and secondary motor cortex, regions that are linked to skeletomotor control and action. Clearly, the two limbs of autonomic control over the stomach are influenced by distinct cortical networks.