The archaeological site of Dodona comprises the sanctuary of Zeus and the acropolis. Located at the foot of the hill, the sanctuary is surrounded by an enclosure; the acropolis occupies the hilltop. Despite its importance, the sanctuary was not heavily built up, and for many centuries worship took place outdoors, with only a simple oikos (house) serving the needs of the ceremony. Building activity increased at the end of the fourth century and particularly during the third century BC, when a number of large buildings, the remains of which are still visible, were constructed.

The sanctuary is defined by an enclosure, whose east section is the extension of the acropolis enclosure. The entrance was on the west section. Next to it was a Doric temple, the altar of Hercules (Building A), and two small Ionic temples dedicated to Dioni, Zeus' wife, the early temple (Building C) and the later one (Building I), built after the destruction of the original temple by the Aetolians. North of the temple of Hercules are the ruins of a basilica, which appears to have had two distinct building phases. West of these temples is the sanctuary's most important building, the Sacred House, or temple of Zeus (Building E1), a square construction with at least four building phases: the original small temple of the early fourth century BC and a number of extensions and reconstructions of the fourth, third, and second centuries BC. The temples of Themis (Building G) and Aphrodite (Building L) flank the temple of Zeus. Pausanias refers to them as 'worthy to be looked upon' (1,17,5), probably because of their central location inside the sanctuary next to the sacred oak and the main temple. North of the temple of Themis, Evangelides excavated a pillaged cist grave, whose date of construction and significance are unknown. Two unexcavated buildings, probably temples, identified southwest of the temple of Aphrodite, complete the amphitheatrical positioning of the temples towards the west. The remaining buildings in the sanctuary's west sector reflect the program of monumental reconstruction orchestrated by King Pyrrhus in the early of third century BC. These are the bouleuterion (Building E2), where the Koinon of Epirus conferred, the prytaneum (Building O), the theatre, and the stadium. The priests' residence (Building M), located between the bouleuterion and the theatre, was the sanctuary's earliest building after the Sacred House; it served as a dwelling for the priests of Zeus or for the leaders of the Koinon of Molossoi.

The ancient acropolis on the hilltop north of the sanctuary probably served as a permanent residence for Dodona's authorities and as a refuge for the locals in times of danger. A fortification wall was erected around the acropolis in the fourth century BC. Built in isodomic masonry and approximately 750 meters long, the wall had rectangular towers along its perimeter, particularly on the more easily accessible west and north sides. It also had three gates: a large one, which communicated directly with the theatre and the sanctuary, in its north-west section, a smaller one in the middle of the south section, and a third gate, which led into the plain of Ioannina, in its east section. The foundations of several buildings and a rock-hewn subterranean water cistern, which supplied the site with water in times of need, were identified inside the acropolis, but have not yet been investigated. Two pillars supported the cistern's ceiling, and its walls were covered with hydraulic cement.