The topographical relationships among the lower cranial nerves, internal carotid artery (ICA), and internal jugular vein (IJV) in the upper parapharyngeal neurovascular bundle remain obscure. Thus, details of the anatomy were examined in human fetus histology. We observed the horizontal histological sections from 20 midterm (9–18 weeks) and 12 near‐term (28–40 weeks) fetuses. At the external skull base, the glossopharyngeal nerve crosses the anterior aspect of the IJV to reach the medially located Hyrtl's fissure in the petrous temporal bone. The nerve crossed the anterior aspect of the ICA medially near or below the first cervical nerve root. Below the hypoglossal nerve canal, the accessory nerve crosses the anterior or posterior aspects of the IJV and moves laterally. During the half‐spiral course, the hypoglossal nerve was tightly attached to the posterolateral–anterior aspects of the vagus nerve and surrounded by a common nerve sheath. The glossopharyngeal ganglia sometimes extended inferiorly to the level of the hypoglossal nerve canal but were absent along the inferior course. The inferior vagal ganglion rarely extends above the occipital condyle. The superior cervical sympathetic ganglion occasionally extends above the first cervical nerve root. The IJV (or ICA) descends to the lateral (or medial) margins of the parapharyngeal neurovascular bundle. The glossopharyngeal (or accessory) nerve crosses the ICA (or IJV) to exit the bundle at the base of the skull (or below the hypoglossal nerve canal). The glossopharyngeal and vagus inferior ganglia differ at each site.