Unlike some han whose control was relatively stable throughout the Edo period (1603–1867), Yamagata changed hands a great number of times during its history.

During the Tokugawa shogunate, in 1600, the Mogami were initially confirmed in their holdings, with an assessed income of 570,000 koku, which was the 5th largest domain in Japan at the time.

Torii Tadatsune died without an heir in 1636, and Yamagata was reassigned to Hoshina Masayuki (with a further reduction to 200,000 koku) until he was assigned to rule Aizu Domain in 1643.

Mizuno Tadakiyo served as Jisha-bugyō and wakadoshiyori in the shogunal administration and in 1862, became a rōjū in the service of Shōgun Tokugawa Iemochi.

During the Boshin War, Yamagata Domain was a member of the Ōuetsu Reppan Dōmei; although its final daimyō, Mizuno Tadahiro was only 13 years old.