Justice June Ross said the current restrictions on his travel and communications with an older sister who has spoken openly in support of Al-Qaeda are reasonable, according to Canadian media.
Khadr, 32, has been living in his native Canada since 2015 when he was repatriated as part of a US deal for a guilty plea, which he has since recanted, saying he just wanted out of Guantanamo.
He sought relief from his bail conditions in order to eventually perform the hajj -- a Muslim pilgrimage to Mecca in Saudi Arabia -- as well as permission to speak freely with his controversial sister, Zaynab.
Zaynab Khadr was investigated a decade ago for terrorist links, but was never charged.
She now reportedly lives in Georgia, making supervised visits with her under his current bail conditions impossible.
Omar Khadr became the youngest prisoner at the US facility in Guantanamo Bay, Cuba following his capture in Afghanistan in 2002.
He was sentenced in 2010 to eight years plus time served for murdering a US soldier with a grenade, attempted murder, conspiracy, providing material support for terrorism and spying, but was later sent home to serve the remainder of his sentence.
He said outside an Edmonton, Alberta courtroom last week that he had not expected his US appeal against his conviction to take this long.
"My sentence initially should have ended this past October, but here I am," he told reporters on December 13.
Khadr's father, a financier for Al-Qaeda who was killed in a clash with Pakistani troops in 2003, had taken his son to Afghanistan as a child.
His lawyers fought for several years to have his status as a minor at the time of the attack recognized. Canada's Supreme Court finally agreed one week before his conditional release in 2015.
In Canada, Khadr married and was accepted into a nursing program, but says his legal woes -- including a civil suit brought by the widow of the special forces soldier he was convicted of killing -- sidelined his studies.
A Canadian government payout of Can$10 million (US$7.5 million) payout to him last year, to settle a lawsuit for having violated his rights, provoked outrage.