From the maxillary artery, the posterior deep temporal artery travels upward, passing between the external pterygoid muscle, a muscle in the jaw, and the temporal muscle, which is on the side of the head. In the infratemporal fossa (a space that lies behind the cheekbone), the artery separates into numerous branches. The infratemporal fossa, in addition to the deep temporal artery, contains the temporalis muscle, auriculotemporal nerve, the deep temporal nerves, and the superficial artery.

In the fossa, the posterior deep temporal artery moves into the temporal muscle, along with the deep temporal nerve. The artery supplies blood to the squamous portion of the temporal bone (located at the top if the temporal bone) and the pericranium (the outer covering of the skull), as well as the temporal muscle. It joins with the middle and superficial temporal arteries and the anterior deep temporal artery.