The nucleus is situated in the caudal portion of the ventrolateral pontine tegmentum. Its axons take an unusual course, traveling dorsally and looping around the abducens nucleus, then traveling ventrally to exit the ventral pons medial to the spinal trigeminal nucleus. These axons form the motor component of the facial nerve, with parasympathetic and sensory components forming the nervus intermedius.

The nucleus has a dorsal and ventral region, with neurons in the dorsal region innervating muscles of the upper face and neurons in the ventral region innervating muscles of the lower face.

Kindling-like hyperactivity of the facial motor nucleus induced by constant stimulation of compressing artery is considered as the predominant mechanism underlying the pathogenesis of hemifacial spasm (HFS).