Passengers will now reach their final destination in a record time of 95 minutes, and the train will take five minutes less in the opposite direction.
The Pendolino can reach its maximum speed thanks to tilting technology on two sections of this route.
"This is a significant step forward for Czech railways, paving the way for higher speeds on future high-speed lines where trains will travel at up to 320 km/h," said Czech Transport Minister Martin Kupka.
Travel times between České Budějovice and Prague have been significantly reduced over the years. While the usual travel time was up to three hours in the first half of the 1990s, the current morning Pendolino can now cover the same route in 90 minutes.