The nearby graves of Aidonia are the first sign of organized human life in the area. There are several Late Bronze Age cemeteries dating from the 15th to 13th centuries BCE. Many sacrificial rites were performed in those days.  The original Sanctuary of Zeus was founded probably in the 12th century BCE, which would make it one of the oldest religious sites in Greece.

The first major building activity dates back to the early 6th century BCE, when the early Temple of Zeus and the Heroon of Opheltes were constructed. The sanctuary only came to life during the summer, when the Nemean Games took place. Towards the end of the 5th century BCE the sanctuary was destroyed and, as a result, in the following years the games were held in Argos.
In 330 BC, the games returned to Nemea; this was probably connected with the panhellenic politics of the Macedonians. The games, one of the four Panhellenic Games of ancient Greece, were held every two years in Nemea, honoring the god Zeus. The Games were a multi-day event featuring a variety of athletic competitions, including the stadion (a sprint race of about 200 meters), the diaulos (a double-stadia race), the pentathlon (a combination of five events), and wrestling. The winner of each event was awarded a wreath made of wild celery, a symbol of victory.

At the same time, the Temple of Zeus was reconstructed, one of the first buildings to combine all three ancient Greek architectural orders (Doric, Ionic, Corinthian); several buildings were also constructed in order to serve more practical needs: the Xenon (=guest-house), the Oikoi, the Bath, the Dining Area and the Houses.
In 271 BCE the games were transferred yet again to Argos and after that, the Nemean sanctuary was gradually abandoned.
In the early-Christian era (late 4th-5th century AD) a large agricultural settlement was created on the site. In AD 453 the emperor Theodosius banned all pagan activities and so began the systematic destruction of the Temple of Zeus: its architectural members were used for the construction of a Basilica with a central nave and one aisle at each side. The settlement was abandoned around AD 580 when Slavic tribes invaded the Peloponnese.

The last early Christian (as documented in the museum)

The violence of the invasion of Slavic tribes that put an end to the Early Christian settlement Nemea, as to so many
places in Greece, was most graphically illustrated in the tunnel of the stadium. Sometime around 585 CE someone
crawled into the partially silted up tunnel and set up life there. He lighted the darkness with lamps, cooked his meals
in coarse pots, buried several bronze coins, and scratched the hopeful “ethereal life” on top of older graffiti on the tunnel wall. His sceletal remains where discovered scattered over an area of 5 m² with his skull against the southern wall of the tunnel. That reveals the remains of a wound to the head, inflicted by a sharp straight-edged instrument, that had partially healed before death. He must have survived the initial onslaught of the Slavs, only to be later discovered in his tunnel refuge.

Rediscovery

First excavations started already in 1766 by French archeologists. 1924 the French handed the site over to the  American School of Classical Studies.

In recent years, the tradition of the Nemean Games has been revived, with modern-day athletes competing in a variety of events, including athletics, wrestling, and pentathlon.