The area was part of the Rombout Patent. The community was founded around 1659. The Village of Wappingers Falls was incorporated in 1871 and included the adjacent community of Channingville. The local waterfall was important for early industrial development.

As mentioned above, one half (closer to 2/3) of the Village of Wappingers Falls is located within the Town of Wappinger. However the large post office which services both municipalities is located in the Village of Wappingers Falls. Thus both the Village of Wappingers Falls and the Town of Wappinger (as well as portions of Fishkill, East Fishkill, Poughkeepsie and Lagrange)all have the same zip code; WAPPINGERS FALLS, NY 12590. This often results in confusion. The Town of Wappinger is 28 square miles. Truckers and travelers often attempt to locate an address in the 1.2 square mile Village of Wappingers Falls when the location they are actually seeking is somewhere in the much larger Town of Wappinger (or portions of Fishkill, East Fishkill, Poughkeepsie and Lagrange).