The current name "Sitka" (derived from Sheet’ká, a contraction of the TlingitShee At'iká) means "People on the Outside of Baranof Island", whose Tlingit name is Sheet’-ká X'áat'l (here contracted to Shee).
Sitka's location was originally settled by the Tlingit people over 10,000 years ago. The Russians settled Old Sitka in 1799 under the name Redoubt Saint Michael (Russian: форт Архангела Михаила, tFort Arkhangela Mikhaila). The governor of Russian America, Alexandr Baranov, arrived under the auspices of the Russian-American Company, a colonial trading company chartered by TsarPaul I. In 1802, Tlingit warriors "clad in animal-headed helmets and armour" destroyed the original establishment, killing four hundred Russians and enslaving the rest, with only a few managing to escape. Baranov was forced to levy 10,000 rubles in ransom for the safe return of the surviving settlers.
Baranov returned to Sitka in 1804 with a large contingent of Russians and Aleuts with the Russian warship Neva. The ship bombarded the Tlingit fort but was not able to cause significant damage. The Russians then launched an attack on the fort and were repelled by Tlingit fighters and marksmen. However, the Tlingit gunpowder reserves had been lost before the Russian assault and the Tlingit were forced to leave the fort.
Following their victory at the Battle of Sitka, the Russians established New Archangel as a permanent settlement named after Arkhangelsk, the largest city in the region where Baranov was born. The Tlingit re-established a fort on the Chatham Strait side of Peril Strait to enforce a trade embargo with the Russian establishment. In 1808, with Baranov still governor, Sitka was designated the capital of Russian America.
Sitka was the site of the ceremony in which the Russian flag was lowered and the United States flag raised after Alaska was purchased by the United States. Russia sold Alaska to the United States for only $7.2 million, at 2 cents per acre, as a result of the sea otterfur trade, which had almost completely exterminated the sea otter population. The flag lowering and raising ceremony is re-enacted in Sitka every October 18, known locally as Alaska Day. Alaska's first newspaper following the Alaska Purchase, the Sitka Times, was published by Barney O. Ragan on September 19, 1868. Only four issues were published that year, as Ragan cited a lack of resources available at the time. The paper resumed publishing the following year as the Alaska Times. In 1870, it moved to Seattle, where the year following it was renamed the Seattle Times (not to be confused with the modern-day newspaper of the same name).
Sitka served as the capital of the Alaska Territory until 1906, when the seat of government was relocated north to Juneau.
The Alaska Native Brotherhood was founded in Sitka in 1912 to address racism against Alaska Native people in Alaska. By 1914 the organization had constructed the Alaska Native Brotherhood Hall on Katlian Street.
Sitka's Filipino community established itself in Sitka before 1929. It later became institutionalized as The Filipino Community of Sitka in 1981.