The castle and chateau complex of Jindřichův Hradec, which has spread over the area of three and a half hectares in the course of the centuries, grew from an original Slavic fortified settlement from the 10th century on a rocky headland above the confluence of the Nežárka River and the Hamerský Brook. The shallow valley incision of the brook was used, in the oldest times, for an artificial water reservoir – the later pond Vajgar, serving for the defence of this important fortress. 
The construction of the mediaeval castle, called “Novum castrum“ (the New Castle) in the oldest preserved historical record from 1220, is connected with the name of Jindřich Vítkovec, the founder of the independent Vítek branch of the Lords of Hradec, which used the coat-of-arms with a golden rose in a blue field. At that time, the round Black Tower and the adjoining palace came into being. The castle, later enlarged into a magnificent chateau, served the Lords of Hradec as their main residence until the family died out in 1604. The members of the family essentially influenced all economic, political and cultural events in this region and representatives of each generation held important positions at the royal court. The importance of the Lords of Hradec was expressed in the gradual enlargement of the residence, from the solid Romanesque-Gothic castle into a majestic Gothic fortress with a complicated artistic solution and flawless fortification. 
In the latter half of the 16th century, under Adam II of Hradec, the castle underwent a radical rebuilding to a representative chateau, after the example of the pretentious palaces of the Italian Renaissance. The castle fortress thus became a luxurious residence that satisfied the most demanding requirements of a Renaissance nobleman. Under the management of Balthasar Maggi and a number of other Italian builders, Adam’s building and the Spanish wing were built in the third courtyard, and both these buildings were linked by great arcades, and behind them, as the crown of the then building activity, a little music pavilion, the Roundel. This grand reconstruction practically completed the architectural development of the complex. Adaptations made by later owners were only of a partial character and almost did not affect the Renaissance shape of the chateau. The last member of the family of the Lords of Hradec married Vilém Slavata of Chlum and at Košumberk in 1602, and after the death of her brother Jáchym Oldřich in 1604, he became the heir of the vast domain as well as the title “the ruler of the House of Hradec”. In Czech history he became known as the royal vice-regent, who was thrown out of the window of Prague Castle in the second defenestration in 1618. 
Over the ninety years of the rule of the Slavata family, the chateau did not undergo any essential construction adaptations. However, in the period of 1678 – 1696 the second arcade wing by the Roundel was built and in front of it the garden fountain was set. 
In 1693, Heřman Jakub Černín of Chudenice acquired the chateau by marrying Marie Josefa of Slavata, who got Jindřichův Hradec as her share of the family heritage. The execution of important state functions and the relationship to the ruling House of Habsburg under the first Černíns brought to Jindřichův Hradec prominent visitors from among the members of the imperial court and other representatives of the European political scene. 
It was under the Černíns that the last major architectural remodelling of the chateau, which concerned the chapel, was carried out. In the years 1709 – 1735, the Gothic chapel of the castle was remodelled in the Baroque style after a design by F.M. Kaňka. 
In 1773, the chateau as well as the town were struck by a vast fire that destroyed a major part of the Renaissance interiors along with artistic collections. Temporarily roofed and abandoned by the lords, the chateau went on deteriorating. It was used as the economic centre of the domain, and the great arcades were turned into stables, the Roundel serving as a wood and game storage room and as stables. 
It was the wave of Romanticism that brought new interest in rescuing the chateau. In 1851, the family archives were brought from the Černín Palace into the remodelled premises of the chateau, which became the basis of the present State Regional Archives, still housed in the second chateau courtyard. In the early 20th century, the Viennese architect Humbert Walcher of Moltheim realised partial repairs and adaptations but some part of the chateau remained without repair. 
The Černíns owned the chateau until 1945, when it was confiscated, pursuant to Presidential Decree No.12/1945. The bad condition of the chateau complex kept on deteriorating and several buildings threatened to collapse. A general reconstruction was started in 1976 and lasted, with intervals, seventeen years. The chateau complex was rescued to the expense of 120 million crowns and reopened to the public in 1993.