The reserve 'Neapolis Scythian' was founded in 2011 at the initiative of the Council of Ministers of the Autonomous Republic of Crimea. The museum's exhibition is located on a well-maintained tourist site where the Southern Palace of Neapolis Scythian stood, the largest barbarian fortress of the Northern Black Sea region from the 2nd century BC to the 3rd century AD, mentioned in ancient epigraphic sources.

The creation of the museum was preceded by a long history of archaeological research. In the early 19th century, the ruins of the ancient fortress on the Kermenčik plateau were actively used for quarrying building stone. In 1827, antiquities collector A. I. Sultan-Krym-Girey Kata Girey noticed a limestone slab depicting a horseman and two marble pedestals with Greek inscriptions on a cart transporting stone from Kermenčik. He purchased these stones and informed the director of the Odessa Museum of Antiquities, I. P. Blahramberg, who conducted small excavations. Fragments of reliefs, several gold plaques, and a fragment of roofing tile with a stamp were found. In 1834, Swiss traveler Frédéric Dubois de Montperé continued the research, inspecting the settlement, creating a new plan, and investigating several tombs and a barrow in the Eastern necropolis.

In 1853, Russian archaeologist Count A. S. Uvarov conducted significant excavations, noting that Neapolis was originally a Greek settlement founded by immigrants from Rhodes but later became the residence and fortress of Scythian kings. In 1926, the construction of a reservoir for water supply to Simferopol led to the destruction of part of the southern defensive wall. The excavations were led by archaeologist N. L. Ernst, who in 1927 investigated several tombs in the Western necropolis. After World War II, large-scale excavations began in the area of the central gates, including studies of the mausoleum of Skilur and the southern defensive wall. A western tower burial of Scythian nobility was discovered, as well as buildings with porticoes and granaries.

From 1954 to 1959, excavations were conducted in the area of the central gates and Eastern necropolis. Megarons and new tombs were discovered. Since 1953, the reconstruction of the water treatment facilities in Simferopol led to the destruction of many objects in Neapolis. The period from 1954 to 1963 was protective in nature, with investigations of the eastern defensive wall and adjacent buildings. The search for the acropolis was unsuccessful.

From 1978 to 1988, the work was led by O. A. Makhneva, who studied ash pit No. 3, suburban areas, and sections of the Eastern necropolis. Until 2011, only small excavations were conducted, but in 2011, at the initiative of the Crimean Republican Committee for the Protection of Cultural Heritage, the Historical and Archaeological Reserve 'Neapolis Scythian' was established. Work began on clearing and reconstructing the Southern Palace and the southern defensive wall with the mausoleum of Skilur.

By the end of 2011, part of the territory was prepared for excursion service and became an exhibition of the reserve, including the southern defensive structures, mausoleums of Skilur and Argot, residential and ritual buildings of the Southern Palace, and a wine-making complex. In 2018, a cantilever gallery for temporary exhibitions was opened in the stone tower above the mausoleum of Skilur. Currently, there is an exhibition 'Terra ARCHAEOLOGICA: Crimea 2016, 2018', dedicated to the results of three years of archaeological research.