The company was able to repair the network overnight and the morning rush went smoothly.
Around 2 pm on Wednesday ticket vending machines, digital signs and the website went down causing "massive problems" and delays countrywide, the spokesperson said. Four hours later, Deutsche Bahn had managed to partially restore the system, but it remained unstable until the early hours of the morning.
Passengers were asked to buy tickets on board trains from conductors.
The cause of the system failure is not clear, Deutsche Bahn said.