The decision is expected to have ramifications for hundreds of other cases of alleged racial and other forms of discrimination in Canada.
Javed Latif, a Canadian citizen, worked in the Pakistani air force for 25 years before moving to Ontario with his family in 1997.
Latif was licensed to fly in both Canada and the United States, but needed to retrain in order to fly new aircraft.
In 2004, Bombardier's pilot training centre in Dallas refused to retrain him, saying U.S. authorities had identified him as a "threat to aviation or national security."
Latif said the U.S. authorities had made a mistake. He reapplied to be trained under his Canadian licence by Bombardier in Quebec, but the company refused, again citing U.S. national security concerns.
In 2008, Latif was taken off the threat list by U.S. authorities, without explanation. After his case was re-examined, he was later able to train with Bombardier.
'Branded as a terrorist erroneously'
Catherine McKenzie, Latif's lawyer, indicated the impact on her client of Bombardier's decision not to train him.
"He said in testimony that he felt he was branded as a terrorist erroneously," she told CBC News. "He wasn't able to work as a pilot for four years."
Latif took the case to Quebec's Human Rights Tribunal. Bombardier argued before the tribunal that there "would have been serious consequences" for Bombardier with the U.S. authorities if they had agreed to train him in Canada.
The tribunal nevertheless found in Latif's favour, saying he had been discriminated against based on national and ethnic origin. It awarded him an unprecedented $320,000 in damages.
The Quebec Court of Appeal overturned that award, sending the case to Canada's top court.
In a release, the Centre for Research-Action on Race Relations said key in Thursday's ruling will be whether the Supreme Court defines a burden of proof for proving racial discrimination: whether the complainant must prove that race or ethnic origin was the cause of discrimination, or a factor in the discrimination.
Bombardier did not respond to requests from CBC News for an interview in advance of the ruling.