In the 13th century the Bishop of Passau gave Waldkirchen the title of a "Markt" (market).

Belonging to the Bishop of Passau's territory for more than 600 years, the city became part of the Kingdom of Bavaria in 1806 and in 1871 of the German Empire.

The last fire was on April 26, 1945, when the 16th Company of Regiment Grossdeutschland, SS Panzer Grenadier Division "Das Reich" arrived from St. Pölten, Austria.

Eight civilians were killed in combat with the 11th Armored Division, and 48 houses and city's historical church were destroyed.

Embedded in the Bavarian Forest, Waldkirchen is close to Prague, Munich and Vienna.