Whereas the war itself did not cause much damage, more than a half of the houses were destroyed in the fire of July 1641. The town renovation extended over several decades. Baroque era again profoundly changed the form of public buildings and private houses in the town, enriched České Budějovice with several ecclesiastical sights and inter alia also with one of the town symbols - Samson's fountain. Maria Theresa's reforms in the second half of the 18th century made České Budějovice the seat of a newly created region. Also the Piarist Order, settling here in 1762 and establishing a Latin grammar school, contributed, to a great extent, to the cultural importance of the town. The town theater was established in the same period as well. In 1785, under the Emperor Joseph II, the bishopric of České Budějovice was founded and not even two decades later the seminary and the philosophical institute started their activities. The 19th century entered the town life especially with revolutionary technical progress and development of modern civil society. Built between 1825 and 1832 as the first one on the European continent, the horse-drawn railway connected České Budějovice with Austrian Linz and along with the Vltava trade run by Vojtěch Lanna accelerated transport in the north-south direction. This fact stimulated development of trade and industry. In 1847 the Viennese firm Hardtmuth brought its enterprise manufacturing pencils and ceramic goods to České Budějovice and the town was thus given its first large factory. So far the small Citizen's Brewery was relocated to Linz suburbs in the vicinity of the railway where it had a perspective of further development. In 1895 its opposite pole, the Czech Joint-stock Brewery, the present Budweiser Budvar, was created making the town famous in many countries worldwide. The 20th century brought a turbulent development. České Budějovice grew in a real economic and cultural metropolis of South Bohemia and in 1949 it became the seat of the newly created Region of České Budějovice. České Budějovice between 1990 and 2000
The social changes after 1989 touched almost all the spheres of the life in the South Bohemian metropolis. In 1990 České Budějovice became a statutory town with a Lord Mayor at the head. Reforms of the state administration caused that the town stopped to be the administrative centre of the region for the period between 1990 and 1999. The church administration was renewed and therefore, after 18 years, the cathedra of České Budějovice was occupied in the spring of 1990 and has been occupied ever since.