The place is first mentioned in the deeds of donation of Gimundi to the abbey of Fulda, in 802. The town`s name means confluence in old German; the prefix Hannoversch, or Hanoverian, was added in the 19th century to help distinguish the town from its similarly-named Prussian neighbour, Minden.
City rights might have been granted during the latter half of the 12th century.
The French inventor Denis Papin built a steam-pump-powered paddlewheel boat, probably pedal-driven in 1704, and as a demonstration used it to navigate down the Fulda River from Kassel to Münden in 1707.
Hann. Münden was the site of the Royal Prussian Academy of Forestry: the city`s botanical gardens with many different trees were primarily established for this academy. Later the academy was merged into the University of Göttingen, moving to a new building on the main campus in 1970.