The GDL union called freight train drivers out on strike at noon (1100 GMT).
Drivers of passenger trains will follow starting at 2 a.m. (0100 GMT) Thursday, the union said.
Deutsche Bahn hopes to keep as many as two-thirds of long-distance passenger trains running, and up to half of scheduled regional trains. States in the former East Germany, where GDL is strongest, were likely to be hardest hit.
The strike will end at 2 a.m. (0100 GMT) Saturday, the union says.
The move marks an escalation by GDL after it staged a 42-hour strike against freight services last week, but left passenger trains running. Previously, it had staged several strikes against commuter trains.
GDL wants a hefty pay increase for train drivers and is insisting that they be given a pay deal separate from that given to other railway employees.
It has rejected a 4.5-percent raise that Deutsche Bahn agreed with two other unions that represent a broader range of railway workers.
Germany's main industry lobby group, the Federation of German Industry, urged GDL to end the strike and return to negotiations. It argued that many companies have no alternative to rail transport.
"GDL is provoking major economic damage," the group's head, Juergen Thumann, said in a statement. "A strike of this length by a small professional group is irresponsible."
Government spokesman Thomas Steg appealed to both sides "not to escalate further, but to show good sense and return to the negotiating table."