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It was founded in conjunction with the construction of the Amur railway in 1910, originally named Pyora after the river on which it stands. It was renamed Gondatti in 1914 in honor of the then-governor of Amur Oblast, Nikolay Gondatti. In 1920, it was renamed Vladimiro-Shimanovsky after Vladimir Shimanovsky, a railway engineer and member of the Red Army who was shot dead in Blagoveshchensk during the Russian Civil War. It was granted town status and its name shortened to Shimanovsk in 1950.
During the construction of the Baikal-Amur Mainline in the 1970s, Shimanovsk saw new growth as a center for production of construction materials.