Golovin was originally an Inupiat village called Chinik.
Golovin was named for Captain Vasily Golovnin of the Russian Navy, who visited Alaska to inspect the workings of the Russian-American Company in 1807-1809, in the Diana, and in 1817-1819, in the Kamchatka, while circumnavigating the world. Lt. Lavrenty Zagoskin, from the Imperial Russian Navy sent to Alaska to scout locations for trading posts, reported the village as "Ikalikguigmyut" in 1842. In 1867, the Mission Covenant of Sweden established a church and school south of the current site of Golovin. Around 1890, John Dexter established a trading post that became the center for swapping prospecting information for the entire Seward Peninsula. Gold was discovered in 1898 at Council and Golovin became a supply point for the gold fields. Supplies were unloaded from ships at Golovin and shipped across Golovnin Lagoon and up the Fish and Niukluk Rivers to Council.
When gold was discovered in what is now Nome, much of the mining and shipping activity moved there and Golovin declined in population.
Reindeer herding was introduced in the area about 1900.