HBRY was formed by railroad holding company OmniTRAX in July 1997 to purchase former Canadian National Railway (CN) rail lines running north from The Pas on two branches, one to Flin Flon and on to Lynn Lake, the other to Thompson and on to the Port of Churchill on Hudson Bay.

Previous owner CN had limited the allowable tonnage to operate on the lines as a result of the light rail and poor track base.

However, the HBRY has been able to successfully operate heavier, longer trains without difficulty, resulting in increased business to the Port of Churchill and from various mines and pulp mills.

HBRY is a vital transportation link in northern Manitoba, hauling ores and concentrates, copper, zinc, logs, kraft paper, lumber, and petroleum products.

This change of port is the reason the rail line, having traveled north-east all the way from The Pas turns abruptly and almost directly north slightly to the west after passing Gillam, at Amery.

On July 27, 2005, heavy rains washed out part of the railroad between The Pas and Pukatawagan; all service over the line, including Via Rail trains 690 and 691, was suspended while repairs took place.

On May 23, 2017, OmniTRAX announced that due to unprecedented flooding, the line was closed indefinitely between Amery and Churchill, pending evaluation of the damages and repairs.

[4] Loss of rail service, both passenger and freight, impacted the tourism industry and imposed other costs on Churchill's already fragile economy.

The position of Canada's Natural Resources Minister, Jim Carr, was that "Omnitrax Inc. had legal obligations to repair the rail line and its tracks, citing a contract that required OmniTRAX to "operate, maintain and repair the entire Hudson Bay Railway Line in a diligent and timely manner until March 31, 2029.