Lieutenant Colonel Jon Jackson, Khadr's military lawyer, had sought a supreme court order to force a lower court to examine the constitutionality of the military tribunal set to try the 23-year-old.
Alternatively, Jackson argued, the high court could issue its own decision on the constitutionality.
On Wednesday, a US appeals court also ruled against Khadr, saying he could challenge the constitutionality of the military commission system in an appeal later if he is convicted.
US forces captured Khadr in Afghanistan in July 2002, when he was just 15 years old.
He is accused of killing a US soldier after throwing a grenade at the end of a four-hour US bombardment of an al-Qaeda compound in the eastern Afghan city of Khost.
Khadr faces charges that include conspiring to commit terrorism and murder.
"I have been used too many times when I was a child, and that is why I am here, taking blame and paying for things I did not have a choice in doing..."
Canada, his birth country, has declined to seek his release from Guantanamo, saying the judicial process at the facility should be seen through.
After sacking his US defence lawyers and refusing a plea deal, the complicated court case it set to begin on August 10.
Khadr told prosecutors: "I have been used too many times when I was a child, and that is why I am here, taking blame and paying for things I did not have a choice in doing but was told to do by elders".
The charges against him were first filed in 2005 and have been dropped and reinstated several times amid legal challenges and revisions to the Guantanamo trials.
Defence lawyers say that during at least 142 interrogations in Afghanistan and Guantanamo, Khadr was beaten, doused in freezing water, spat on, chained in painful positions, forced to urinate on himself, terrorised by barking dogs, subjected to flashing lights and sleep deprivation and threatened with rape.
Prosecutors contend Khadr was treated humanely and has fabricated the abuse allegations.
Toronto born Khadr is the youngest of the 176 prisoners still held at the US military prison in Cuba. If convicted, he could face life in prison.