In the second half of the 13th century, a Gothic castle was built at the site. During its history, the castle was rebuilt several times. It was first expanded during the Renaissance period, then rebuilt into a Baroque castle at the order of Adam Franz von Schwarzenberg in the beginning of the 18th century. It reached its current appearance during the 19th century, when Johann Adolf II von Schwarzenberg ordered the reconstruction of the castle in the romantic style of England's Windsor Castle.
The Schwarzenbergs lived in Hluboká until the end of 1939, when the last owner (Adolph Schwarzenberg) emigrated overseas to escape from the Nazis. The Schwarzenbergs lost all of their Czech property through a special legislative Act, the Lex Schwarzenberg, in 1947.
Hluboká Castle is a National Cultural Monument of the Czech Republic.