Via Rail temporarily suspended service on Train 692 between Thompson and Churchill on Wednesday due to flooding.
It says that forced a train to stop suddenly in Thompson.
About 90 passengers spent part of Wednesday and most of Thursday stuck on a train, parked at the station in Thompson.
A VIA rail spokesperson told CTV News in an email Thursday evening that staff are on board the train, providing food and refreshments.
A little more than half of the passengers will be flown on two charter planes to Churchill Thursday night.
On Friday, Via said the track between Thompson and Churchill had re-opened.