The train operator said that traffic was "generally stable" following the end of the 14-hour strike at 4am.
But with many trains and drivers still out of position on Thursday, there were additional delays and cancellations for passengers in the morning.
Running a reduced long-distance timetable before the strike began on Wednesday allowed DB to get many trains ready for services to restart.
Only one third of intercity services ran after the train operator introduced an emergency timetable in advance of the strike.
Berlin S-Bahn trains were also running less frequently than usual early on Thursday morning, with the S45 line remaining completely out of service.
The German Train Drivers' Union (GDL) called the strike, its second in eight days, over a dispute with DB regarding pay and labour representation.
It is demanding a five percent pay increase for its members and the right to represent conductors and other on-board staff as well as train drivers.
Passengers can check on delays in their region using DB's interactive map here, or call the hotline on 0180 699 6633.