People settled in the area from the 5th to 4th millennium BC, as witnessed by the archeological traces of the Narva culture, named after the city. The fortified settlement at Narva Joaoru is the oldest known in Estonia, dated to around 1000 BC. The earliest written reference of Narva is in the First Novgorod Chronicle, which in the year 1172 describes a district in Novgorod called Nerevsky or Narovsky konets (yard). According to historians, this name derives from the name of Narva or Narva River and indicates that a frequently used trade route went through Narva, although there is no evidence of the existence of a trading settlement at the time.

When Estonia regained its independence in 1991, Narva became again a border city. As the population of Narva was dominated by Soviet-era migrants from Russia and other union republics, the fall of the Soviet Union and re-established Republic of Estonia were not especially greeted in the city and other industrial towns of the Ida-Viru County. The dissatisfaction culminated with the so-called Narva referendum of 16–17 July 1993, which proposed autonomy for Narva and Sillamäe, another nearby industrial town. The Estonian government deemed the referendum illegal and sent Indrek Tarand as its special envoy to the region. The referendum was indeed carried out, but generally failed as it did not provide a clear popular mandate for the autonomy, leading to the stabilization of the situation.

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