The settlement was established at the end of 12th century. First written document mentions Stonařov in 1347. In 1367 it received township privileges. In 1530 the owners of the town sold it to neighbouring Jihlava.
The main trade and post road between Prague and Vienna built in 1750 went through Stonařov. In 1850 Stonařov had 2,009 inhabitants; during the next decades the population decreased.
The municipality was damaged by large fires in 1900 and 1901. Before World War I the place was a target of tourists from Vienna. German-speaking inhabitants were expelled after the end of World War II.
Agriculture and small-scale textile production were the main sources of income, though at the end of the 19th century two textile manufacturies were built here.