In prehistoric times the lands of the canton were inhabited by people of the Pfyn culture along Lake Constance. During Roman times the canton was part of the province Raetia until in 450 the lands were settled by the Alamanni. In the 6th century Thurgovia became a Gau of the Frankish Empire as part of Alemannia, passing to the Duchy of Swabia in the early 10th century. At this time, Thurgovia included not just what is now the canton of Thurgau, but also much of the territory of the modern canton of St. Gallen, the Appenzell and the eastern parts of the canton of Zurich.

The most important cities of Thurgovia in the early medieval period were Constance as the seat of the bishop, and St. Gallen for its abbey. The dukes of Zähringen and the counts of Kyburg took over much of the land in the High Middle Ages. When the Kyburg dynasty became extinct in 1264 the Habsburgs took over that land. The Old Swiss Confederacy allied with ten freed bailiwicks of the former Toggenburg seized the lands of the Thurgau from the Habsburgs in 1460, and it became a subject territory of seven Swiss cantons (Zurich, Lucerne, Uri, Schwyz, Unterwalden, Zug and Glarus).

During the Protestant Reformation in Switzerland, both the Catholic and emerging Reformed parties sought to swing the subject territories, such as the Thurgau, to their side. In 1524, in an incident that resonated across Switzerland, local peasants occupied the cloister of Ittingen in the Thurgau, driving out the monks, destroying documents, and devastating the wine-cellar. Between 1526 and 1531, most of the Thurgau's population adopted the new Reformed faith spreading from Zurich; Zurich's defeat in the War of Kappel (1531) ended Reformed predominance. Instead, the First Peace of Kappel protected both Catholic and Reformed worship, though the provisions of the treaty generally favored the Catholics, who also made up a majority among the seven ruling cantons. Religious tensions over the Thurgau were an important background to the First War of Villmergen (1656), during which Zurich briefly occupied the Thurgau.

In 1798 the land became a canton for the first time as part of the Helvetic Republic. In 1803, as part of the Act of Mediation, the canton of Thurgau became a member of the Swiss confederation. The cantonal coat of arms was designed in 1803, based on the coat of arms of the House of Kyburg which ruled the Thurgau in the 13th century, changing the background to green-and-white, at the time considered "revolutionary" colours (c.f. tricolour); as the placement of a yellow (or) charge on white (argent) is a violation of heraldic principles, there have been suggestions to modify the design, including a 1938 suggestion to use a solid green field divided by a diagonal white line, but they were not successful.

Swiss History Timeline - Thurgau
Thurgau coat-of-arms