Sušice originated as a settlement near the Otava River, a gold-mining area. The settlement was probably founded around 790, however the first written mention is from 1233. In the 12th century was Sušice owned by the Bavarian Counts of Bogen. It was re-connected to Bohemia by the Czech king Ottokar II of Bohemia in the 13th century and after 1260 it became a royal fortified town.

During the Hussite Wars in the first half of the 15th century Sušice was a Hussite town. After the Battle of White Mountain most of the properties were confiscated. The destruction of the town was finished by fire in 1707, when most of the sites burned down.

In 1683, a baroque chapel was built on what is now the edge of the town. This chapel still stands and is somewhat fortress-like in its appearance with its outer walls set in a square formation and the chapel located in the centre.

Until 1918, Sušice - Schuttenhoffen was part of the Austrian monarchy (Austrian side after the compromise of 1867). The town was an administrative seat of the district of the same name, one of the 94 Bezirkshauptmannschaften in Bohemia.