The origins of this charming town, which spreads out in the midst of fishpond plains, date from about the middle of 12th century when a small market settlement, or perhaps a farmstead, was established on a path running through deep border forests. The fact that the place must have been first cut and cleared (or 'refined') probably gave this settlement its name Třeboň (from tříbit - to refine).This vast area was granted by the Czech king as a dominion to the first known member of the lately extended 'House of Vítek' family, namely Vítek of Prčice. Very soon after its foundation, the settlement gained the possession of the Cistercian monastery in the upper-Austrian town of Světlá (Zwettl). Later, at around 1250, these estates were bought back by Sir Pelhřim and Sir Ojíř, brothers from the Landštejn branch of the House of Vítek. By 1300, it is presumed that Třeboň had been fortified with walls and a moat. The settlement developed quickly, and records of the church of St. Jiljí already existed from as early as 1280. Třeboň became the centre of a rapidly expanding dominion. In 1341, Třeboň is quoted as a borough and, in 1366, its Czech name appeared instead of the previously used 'Witigenowe' or 'Wittingau' (Vítkův Luh). In 1366, the noble brothers of Rožmberk became the new owners of Třeboň and the surrounding lands and, under their rule, Třeboň became an important and wealthy town. Early in the following year, the brothers of Rožmberk founded a monastery in Třeboň and in 1376 the town was granted the rights of a Royal Free City. In 1378, on the basis of the recommendation of the Rožmberk brothers, a Royal privilage concerning imports of salt was granted to the town of Třeboň by the Czech King, Charles IV. By the end of the 14th century, the town had strong walls, a chateau, and a moat. These, along with the surrounding boggy land, made Třeboň a town very difficult to conquer. Even during the Hussite wars, the town managed to stop several attacks.
The period of greatest growth for the town dates back to the second half of the fifteenth century when Petr IV of Rožmberk (1462 - 1523) seriously began to take care of the land. It was one of his subjects, one Štěpánek Netolický, who first made the district renowned as a fishpond farming area. The foundation of a new brewery in 1505 was another significant occurance. The sixteenth and the beginning of the seventeenth centuries saw the greatest years of prosperity for the town, especially under the rule of the brothers Vilém and Petr Vok, the last two Lords of Rožmberk. Much attention was paid to the economic development of the whole estate, particularly the fishpond farming and the brewery. The natural disposition of the Třeboň valley provided a good opportunity for the founding of numerous new fishponds on a larger scale and this resulted in an enrichment of the whole economy of this area. A new era of building and construction began with the head of all entrepreneurial activities of the Rožmberk lords, Sir Jakub Krčín of Jelčany. His economic reforms have left many remarkable traces on the town of Třeboň and the surrounding lands. In 1602, Třeboň became the headquarters of the House of Rožmberk, the most powerful south Bohemian House at that time. In 1611, after the death of Petr Vok, the last Rožmberk, both the estate and the town were inhereted by the Švamberks, who later lost it due to their participation in the uprising of the Estates against the Hapsburgs. The whole estate was confiscated and Třeboň came under the rule of the House of Hapsburg between the years 1622 and 1660. In 1660, Jan Adolf, Duke of Swarzenberg, was given the Třeboň estate as a personal reward for his service. The Swarzenbergs, who kept possession of the estate until the 20th century, really favoured the town.
Třeboň took a long time to recover from the substantial damages caused by wars and several disasterous fires over the years, which left the town much altered in appearance. Only in the middle of the 19th century was some degree of restoration undertaken, when Třeboň became a district town following the constitution of an administrative and court district here. Another impulse for further flourishing of the whole region was the construction of a number of important thoroughfares, particularly the construction of the railway in 1871 which included a line to Vienna. Important developmental changes took place following World War I, when all the properties of the House of Swarzenberg were nationalised as a result of the 1st land reform. Following World War II, despite further losses to the towns population, the first important industries were established, namely a textile factory and large-scale agricultural production. In 1960, the District of Třeboň was abrogated and the town of Třeboň was given the status of a Spa Town.