Brunntal was first mentioned in 1222, when a donation to the Neumünster in Würzburg was recorded. A local nobility is mentioned in a deed of 1352; also the monastery Bronnbach had at that time possession in Brunntal. Around 1537, the landgraves of Leuchtenberg had possessions in Brunntal.
At the beginning of the Thirty Years' War, the plague raged in Brunntal and left only seven people alive. A shrine from 1624 at the boundary to Wenkheim reminds of it.
Brunntal belonged until 1803 to Kurmainz, then briefly to the Principality of Leiningen and was finally incorporated in 1806 in the Grand Duchy of Baden. As part of the Baden-Württemberg municipal reform was on 31 December 1973 from the previously independent municipalities Brunntal, Wenkheim, Werbach and Werbachhausen the new municipality Werbach formed in the Main-Tauber-Kreis.
In one of the state of Baden-Württemberg financially supported large village renovation from 1984 to 1994, the municipality and almost all households participated. With Brunnenplatz and Bildstockplatz two town centers were created. In 1992, Brunntal took part in the state competition Our village should be more beautiful and scored the first place (out of 26 applicants). In the re-participation in 1993 Brunntal finished third.