Fladungen first appears in a public record in 789 AD; the town was granted "Stadtrechte" (city rights) by Louis IV, Holy Roman Emperor, in 1335.

From the 16th century onwards it was part of the Prince-Bishopric of Würzburg; the town coat of arms still shows the figure of a bishop with a sword and crozier, symbolizing the Prince-Bishop's combination of religious and secular power.

The region around Fladungen was religiously contested during the Reformation, the Counter-Reformation and the Thirty Years War, but ultimately the town became predominantly Catholic, and remains so today.

From the 18th to the mid-20th century, Fladungen was the primary market town for the Franconian Rhön, a relatively rural and underpopulated region whose economy was dominated by agriculture, sheep-herding and timber.

Fladungen is noted for the "Freilandmuseum", an open-air museum of historical houses that includes more than a dozen farmhouses as well as a church and a mill.