The founding of this castle is originally associated with the Čéč clan who founded old Budějovice, even though its original name of Fronburg (Master's castle) attests to its probable establishment as an agricultural estate.
Hluboká entered history in 1285 when Vítek, brother of Záviš of Falkenštejn, ruled the estate. After Záviš was accused of grand treason, Vítek refused to hand Hluboká over to royal hands and the Duke of Opava Mikuláš had Záviš executed in front of Hluboká, on the so-called “field of penalty”.
The Hluboká estates were often used afterwards for securities and pledges and slowly dilapidated, then were finally repaired by Vilém of Pernštejn, who also had a series of lakes and ponds built around Hluboká, including Bezdrev. In 1561 Jáchym of Hradec bought Hluboká from the royal chamber. The building work he began was continued after his premature death by his son Adam with the participation of the Italian builder Baltazar Maggi, who reconstructed the Gothic castle into a Renaissance chateau around two courtyards.
The next construction work done of Hluboká was at the beginning of the 18th century, when Adam Franz of Schwarzenberg had the castle reconstructed from the foundations up according to a design by the court builder Pavel Ignác Bayer. Today's appearance, however, comes to us from the time of Johann Adolf II. of Schwarzenberg and his wife Eleonora. The royal pair often made trips to England and became acquainted there with Tudorian and Elizabethan architecture. The princess especially was so charmed by the royal chateau of Windsor that upon their return the Viennese architect Franz Beer was commissioned to reconstruct Hluboká based on its design. The work lasted from 1839 - 1871 and completely covered all traces of previous building phases. At the same time, the extensive area in front of the castle was demolished and an English park was installed with a winter garden and adjacent riding school. On the west side of the castle a court administration building was constructed in the same style.