The court refused Thursday to hear the appeals of Jeremy Hinzman and Brandon Hughey, who were rejected by Canada's Immigration and Refugee Board in 2005.
The board ruled they would not be at risk of their lives if they returned to the United States, nor were they at risk of "cruel and unusual treatment or punishment."
Hinzman and Hughey deserted the U.S. Army in 2004 after learning their units were to be deployed to Iraq to fight in a war they have called immoral and illegal. The men argue that serving in Iraq would force them to commit crimes against civilians, and that they would be persecuted if forced to return to the United States.
Both the Federal Court and the Federal Court of Appeal have refused to review their cases.
As is usual in such cases, the Supreme Court gave no reasons for its decision Thursday.
Hinzman fled from Fort Bragg, North Carolina, with his wife and son in January 2004, weeks before his 82nd Airborne Division was due to go to Iraq. He had served three years in the U.S. Army, but had applied for conscientious objector status before his unit was sent to Afghanistan in 2002.
The 20-year-old Hughey was part of the 1st Cavalry in Fort Hood, Texas, and fled to Canada in March 2004.
Both would face jail time if convicted of desertion.
Hinzman and Hugley's defense lawyer Jeffry House noted earlier this year that about 20 U.S. military personnel have applied for refugee status in Canada. He estimated as many as 200 American war resisters were hiding in Canada, waiting to see how Hinzman's case is played out before coming forward.