Devices, systems and methods are disclosed for modulating cranial nerves, such as the sphenopalatine ganglion, to treat a medical condition of a patient, such as cluster headache. A stimulation device is advanced transnasally to a target site at or adjacent to the nasopharyngeal mucosa posterior to the middle turbinate. Electrical impulses are applied through one or more electrodes in the stimulation device to the target nerve sufficient to modulate the nerve and treat the medical condition.