The distributed denial of service (DDoS) attack initially caused problems with the railway's website and its widely used DB Navigator app on Tuesday afternoon.
The website and app issues were mostly resolved by Tuesday evening, but problems resurfaced again on Wednesday morning.
Customers have been having problems searching for rail connections and trying to book tickets.
A statement from the rail operator said: "The current attack is specifically targeting DB and has been carried out in waves. The extent is considerable."
Deutsche Bahn, Germany's state-owned rail service, operates both passenger and cargo trains as well as suburban commuter railways in many cities.
The operator said its defence measures were working to minimise impact on customers.
The company has been in contact with Germany's BSI cybersecurity authorities, an interior ministry spokeswoman said Wednesday, adding that she could provide few additional details about the attack.
"The protection of customer data and the availability of our information and booking systems remain our top priority," Deutsche Bahn said.
A DDoS is a digital overload attack, which involves thousands of hijacked computers or devices simultaneously sending many requests to a website or app so that it crashes.
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