Ancient Elis, the largest city and capital of the homonymous city-state, was built on the north banks of the Peneus River, between the mountainous part of Elis (Akroreia) and its coastal lowlands (Elis Koile). The site was inhabited almost continuously from the beginning of the Middle Palaeolithic (130/120,000) until the end of the Early Byzantine period (seventh century AD), when the city was abandoned. Aetolos Oxylos is considered the city's mythical founder (twelfth-eleventh centuries BC). He allegedly took advantage of the Dorian invasion in order to subordinate the area's early inhabitants and founded the first settlement. The city thrived in the early historical period (eleventh-tenth centuries BC), during the late Archaic and early Classical periods (sixth-fifth centuries BC), and in the Early Roman period (second century BC - early third century AD).


Large numbers of flint tools from surface layers suggest that the site was inhabited since the Palaeolithic. Habitation concentrated primarily in the area of the later theatre at the end of the Neolithic, and on the acropolis during the late third and early second millennia BC. The Mycenaean period saw the development of several settlements, whose cemeteries lie close to the limits of the later city. Several graves in the later city's agora date from the end of the Mycenaean period (mid-twelfth century BC).


The graves at the theatre and neighbouring east cemetery date to the early historical period, the so-called Dark Age (eleventh-tenth centuries BC). The corresponding settlements were probably located nearby. The Geometric finds, which indicate the possible existence of two small temples, are limited, and there is even less evidence for the seventh century BC. By contrast, the sixth century BC was a period of development witnessed by the finds from temples and public buildings. The introduction of democracy, the city's establishment as capital of the homonymous city-state, and its merger with the surrounding small settlements (471 BC) were landmarks in the history of Elis.


During the Peloponnesian War, the city's long-lived alliance with Sparta came to an end with devastating consequences for Elis. King Agis of Lacedaemon marched against Elis in 399 BC, King Philip II of Macedon supported the establishment of oligarchy and abolished democracy in 343 BC, and Telesphoros conquered the city in 313 BC. Aided by Roman troops, the city guard repelled an attack by King Philip V of Macedon in 209 BC, and in 191 BC, Elis joined the Achaian League. In 146 BC, it was conquered by the Romans and became part of the Roman province of Achaia; it came under the full authority of the Roman Empire as part of the Provincia Macedoniae in the early first century BC.


Elis thrived in the Early Roman period and enjoyed numerous privileges because of its role in the organization of the Olympic Games. It was greatly influenced by Roman civilization and developed a multi-cultural identity due to the various ethnic groups, particularly Romans, living there.


The barbarian invasions of Late Antiquity did not spare Elis. The city was raided by the Heruli (267 AD), the Visigoths (395 AD), and the Vandals (467 AD) before it was destroyed by two earthquakes in the sixth century AD. Life continued, however, during the seventh century, towards the end of which the city was definitively abandoned. Sporadic habitation among the ruins of the ancient city occurred in later centuries.


Elis was the birthplace of several important figures of the ancient world, including Iphitus, who established the first Olympic Games (ninth or eighth century BC), the sophist Hippias (fifth century BC), and the sceptic Pyrron (365-275 BC).


Elis was first excavated in 1910-1914 by the Austrian Archaeological Institute, whose director for the period 1911-1914 was Otto Walter. The Greek archaeologist Anastasios Orlandos participated in these early excavations. Nikolaos Gialouris resumed the excavations in 1960 for the Greek Archaeological Society. Recent work for the promotion of the archaeological site of Elis includes the removal of undergrowth, tree planting, the creation of visitors' paths, the installation of signs with explanatory texts, and the conservation and restoration of its monuments.