Trains were again put into operation after the management and engine drivers' trade union reached agreement on conditions for their work on Friday.
The railway company's spokesman Samir Kardic said that the union's demand on revoking a regulation that only one driver will be on the locomotive was accepted.
The decision to introduce trains with one crew member was made as part of cost-cutting measures, which engine drivers see as totally inappropriate.
The train service interruption affected the work of big companies including the Aluminij plant in Mostar and the steelwork in Zenica that obtain raw material from the Croatian seaport of Ploce by train.