The aim of this study was to develop a technique for recording electrical activity of the equine cerebral cortex following application of a noxious electrical stimulus to the maxillary branch of the trigeminal nerve in order to investigate trigeminal nerve neurophysiology in control and headshaking horses. Triphasic somatosensory evoked potentials (SEPs) were recorded using subcutaneous needle electrodes in four control and four headshaking horses under general anaesthesia. Dural electroencephalography electrodes were used to record SEPs in one further control and one further headshaking horse. Headshaking horses appeared to have decreased middle latency and inter-peak intervals following stimulation of the trigeminal nerve compared with control horses, supporting abnormal trigeminal nerve physiology in equine headshaking.