We investigated the effects of water swallowing, pharyngeal stimulation and oro-pharyngeal anesthesia on corticobulbar and craniobulbar projections to human swallowing musculature. Changes in pathway excitability were measured via electromyography from swallowed intra-luminal pharyngeal and esophageal electrodes to motor cerebral and trigeminal nerve magnetic stimulation. Following both water swallowing and pharyngeal stimulation, pharyngo-esophageal corticobulbar excitability increased (swallowing: pharynx = +59 ± 12%, p<0.001; esophagus = +45 ± 20%, p<0.05, pharyngeal stimulation: pharynx = +76 ± 19%, p<0.001; esophagus = +45 ± 23%, p=0.05), being early with swallowing but late with stimulation. By comparison, craniobulbar excitability increased early after swallowing but remained unaffected by pharyngeal stimulation. Following anesthesia, both corticobulbar (pharynx = -24 ± 10%, p<0.05; esophagus = -28 ± 7%, p<0.01) and craniobulbar excitability showed a late decreased. Thus, swallowing induces transient early facilitation of corticobulbar and craniobulbar projections, while electrical stimulation promotes delayed facilitation mainly in cortex. With removal of input, both corticobulbar and craniobulbar projections show delayed inhibition, implying a reduction in motoneuron and/or cortical activity.