Service along the 270-kilometre stretch of track between Gillam and Churchill shut down on June 2 after several freight cars derailed.
Freight service eventually resumed but Via Rail's passenger service has been off since the accident.
Via Rail says a train is scheduled to leave Gillam tonight for Churchill and another is to depart from Churchill on Saturday.
The rail line crosses sub-arctic terrain and is frequently hit with disruptions.
Omnitrax Canada, which owns the line, wants to conduct test runs of crude oil shipments along the line, but the plan is facing strong opposition from environment groups and the Manitoba government.