There were no immediate reports of damage or casualties.
The quake was followed by multiple aftershocks Monday morning, including a quake that the USGS says was even larger.
Following the Monday quakes, the Yukon government issued messages via Twitter confirming that the school in Ross River, about 200 kilometres northeast of Whitehorse, remains closed as engineers check for safety.
"We were shaken violently out of bed", Stanford said.
Heath Scott, chief of police in Haines, about 60 miles (96.5 kilometers) southeast of the quake epicenter, said it shook a picture frame off his file cabinet.
Outside of British Columbia, three earthquakes above six in magnitude hit the Northwest Territories between 1985 and 1988 while the forth happened in Northern Quebec in 1989 and measured in at a 6.3 magnitude.
Seismologist Natalia Ruppert warned that more aftershocks are expected over the next few days.
It was centred in a remote area 77 kilometres northwest of Skagway, Alaska, and 127 kilometres southwest of Whitehorse.
There have also been a number of aftershocks, with magnitudes of between 2.5 and 5.2. According to the University of Alaska Fairbanks' Alaska Earthquake Center, it had a magnitude of 6.2.
CBC reported power was knocked out in Whitehorse, Yukon, 80 miles to the northeast, and one resident said the shaking lasted 30 seconds.
Quake seismologist Alison Bird of the Geological Survey of Canada said continued shaking is expected.