The GDL union called a warning strike from 6:00 pm (1600 GMT), saying it would primarily affect freight trains rather than passenger trains so as to spare commuters.
Deutsche Bahn is demanding that GDL sign a cooperation agreement with the group's own in-house union EVG.
The two unions are at loggerheads over which groups of personnel they should represent.
German air passengers faced a half-day of delays and cancellations on Friday as pilots of the low-cost carrier Germanwings, a subsidiary of Lufthansa, walked out in a long-running dispute over early retirement provisions.