Situated in the southern portion of the city enclosure of Nekhen stood the great temple to the city's falcon god, Nekheny or The Nekhenite. The temple itself covered approximately one-sixth of the total area and it would have dominated not only the temple complex, but the town itself. One of the greatest finds to come from the Temple Complex was a cache of ceremonial items which included a palette and macehead belonging to Narmer, a macehead of Scorpion II, statues of Khasekhem and a great golden head of a falcon, all found during the earliest excavations of the area.

While not much remains of the early temple, through excavations archaeologists have been able to ascertain the layout of the complex and what the temple would have looked like. The centerpiece of the complex would have been a three-room shrine, its facade made of four huge timber pillars that would have stood at least 20 feet high and its walls lavishly appointed with colored mats. In front of the shrine would have been a large oval courtyard in which stood a solitary pole displaying the image of the falcon god. At its base were makeshift platforms, used by the early kings to make sacrifices to Nekheny of new-born goats, cattle, crocodiles and even fish. Around this courtyard stood little workshops where trained craftsmen created luxury goods for their royal patrons and their gods, producing ivory boxes, polished stone jars, jewelry and ceremonial weapons - perhaps even those that were found in the cache.

From this we can see that the Temple and its complex was not only important to the residents of Nekhen for strictly religious purposes, but that it also contributed to the growth of the city as a whole. It is in this place that the ancient kings of Upper Egypt would have worshipped their patron god and, standing on the platforms, could have viewed the breadth of their kingdom. Even though the city of Nekhen began to decline during the First Dynasty, the Temple of Nekhen still retained its status as an important religious center throughout the following years. The Temple itself was rebuilt during the 4th Dynasty and the excavation of statues of Pepi and his son, Merenre, attest that the Temple was still honored. The Temple's god, Nekheny, was not forgotten either - although later assimilated into the Cult of Horus, a special title, that of Horus the Nekhenite, still gave evidence of its origins and the Greeks knew the city of Nekhen by the name Hierakonpolis, or City of the Hawk.