Until after the Meiji Restoration, the area that is now Niigata Prefecture was divided into Echigo Province and Sado Province. During the Sengoku period, the Nagao clan, who were at times vassals to the Uesugi, ruled a fief in the western part of modern Niigata from Kasugayama Castle. The most notable member of the Nagao clan was Nagao Kagetora, later and better known as Uesugi Kenshin. He unified the leaders of Echigo Province and became its sole ruler. By taking the surname Uesugi, he also became the head of the Uesugi clan and effectively brought their realm under his control.
The city of Niigata is now the largest Japanese city facing the Sea of Japan. It was the first Japanese port on the Sea of Japan to be opened to foreign trade following the opening of Japan by Matthew Perry. It has since played an important role in trade with Russia and Korea. A freighter from North Korea visits Niigata once a month, in one of the few forms of direct contact between Japan and that country.
The Etsuzankai organization, led by the politician Kakuei Tanaka, was highly influential in bringing infrastructure improvements to Niigata Prefecture in the 1960s and 1970s. These included the Jōetsu Shinkansen high-speed rail line and the Kanetsu Expressway to Tokyo.
On January 9, 2006, a heavy winter storm struck the prefecture and its neighbors. At least 71 people died and more than 1,000 were injured. Also in 2006, a massive tsunami and earthquake damaged homes and caused casualties in the maritime areas of Niigata Prefecture, especially near Sado Island.
On July 16, 2007, another earthquake hit the area.
Niigata Prefecture hosts the Fuji Rock Festival, an annual event held at the Naeba ski resort. The three-day event, organized by Smash Japan, features more than 200 Japanese and international musicians. It is one of the largest outdoor music events in Japan, with more than 100,000 people attending in 2005.