Kunya Urgench is an ancient settlement that emerged around the 5th century BCE and existed until the 17th century CE. The exact founding date of Urgench is not established. Archaeologists have discovered ancient settlement remains on the territory of the site. Excavations of the hill known as Kyrkmolla revealed the outlines of a powerful ancient fortress built on earlier cultural layers with ceramics dating back to the 5th-2nd centuries BCE. Undoubtedly, this is the original core of the city with robust fortifications. The inscription of King Darius I in the Behistun Inscription, which mentions Khwarazm as one of the twenty-three countries subject to the Achaemenid Empire, also attests to human habitation in this area in the 1st millennium BCE.

In 712 CE, the entire Khwarazm region was conquered by the Arabs, and Urgench was renamed as Jurjaniya in Arabic style. It quickly grew in importance due to its favorable location at the crossroads of trade routes. In 995 CE, the ruler al-Mamun ibn-Muhammad managed to conquer Khwarazm and overthrow the local Muslim dynasty, reuniting the region and assuming the title of Khwarazmshah. In the early 11th century, after a period of turbulent military events, distant campaigns, and complex political intrigues, the reign of Mamun I, followed briefly by his eldest son Ali ibn-Mamun, gave way to a brilliant period of rule under his other son, Mamun ibn-Mamun. It was during his reign that a unique circle of scholars, known as the "Academy" of Mamun, flourished in Urgench, overshadowing the fame of Bukhara, the capital of the defeated Samanids. The Academy was adorned by the great encyclopedist Abu Rayhan al-Biruni (973-1050) and the brilliant naturalist, physician, and philosopher Abu Ali ibn Sina (980-1037), known in the West as Avicenna. This prosperous period in the city's history did not last long: the enlightened monarch Mamun II perished in 1017 when Khwarazm was conquered by Sultan Mahmud of Ghazni, and a quarter of a century later, the victorious Seljuks took control of all the territories of the Ghaznavids. From 1044 CE, Khwarazm became nothing more than a province of the Great Seljuk state.

Bright traces of the Khwarazmshah era remain at the Kunya-Urgench site in the form of archaeological and architectural monuments. The most notable among them are the unique mausoleums of Il-Arslan and Tekesh. In the first half of the 14th century, Kutlug-Timur and his wife Turabek-khanym played a significant role in the development of the city. Under their patronage, the surviving monuments from the pre-Mongol period were restored, including the 11th-century minaret at the mosque-namazgah, which became one of the tallest in the world (about 60 meters). A substantial area within the city walls, with a length of up to 10 kilometers, was built and remained as a rampart. It stretches north from the fortress of Ak-Gala, encircles the entire territory of the present-day reserve, and turns south toward the fortress of Khorezm-Bag. The waters of the Amu Darya (Darya-Lyk Canal) flowed near the southern wall. It was during this period, most likely, that the mausoleum of Turabek-khanym was built, a true masterpiece of medieval architecture that has survived to this day.

After 1360 CE, an independent dynasty called Sufi settled in Urgench, separate from the Golden Horde, and by this time, the process of Turkicization of the Khwarazmians' language had apparently been completed. In 1388 CE, a new catastrophe struck when Timur devastated Urgench, destroying most of the buildings and deporting the remaining population to Samarkand. After this event, the city never recovered.