Emergency services said the crash had occurred in a region around 132 km (82 miles) south of the capital Prague. Images showed mainly damage to the front ends of the trains where they hit head-on.
Firefighters had to free the driver of one of the trains, the CTK news agency reported.
A spokeswoman for a regional hospital told CTK that four people had been admitted with serious injuries.
Nine people suffered moderate injuries and 25 others were lightly hurt, the region's governor, Martin Kuba, told Czech television.
Transport Minister Martin Kupka said on X that the crash was still under investigation but preliminary information suggested that one of the trains had probably passed a signal in the stop position.
(Reporting by Jason HovetEditing by Alexandra Hudson and Gareth Jones)
The rising sun silhouettes a skyline dominated by the Church of our Lady in front of Týn from the Petrin Hill in Prague, Czech Republic, 10 April 2017. Meteorologist predict the cloudy weather with temperatures around 10 - 13 degrees Celsius in the next days in the Czech Republic. EPA/MARTIN DIVISEK 