El Mahdi Jamali and Sabrine Djaermane, both 18, appeared briefly in court to face the accusations, which include using explosives and conspiring with a terrorist group.
The Royal Canadian Mounted Police (RCMP) said in a statement that the pair "were planning to leave the country to commit a terrorist act abroad."
No details of their alleged crimes were disclosed.
The RCMP said their investigation is ongoing, specifically to determine if others were involved in the alleged plot, which was exposed by a tip to police.
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The school was also apparently attended by five of seven people who recently traveled to Turkey en route to Syria, where they planned to join Islamic State militants, according to some of the youths' parents.
It was also linked to Adil Charkaoui, a Moroccan-born Canadian who years ago successfully challenged his detention without trial under a controversial security measure over suspicions that he was an Al-Qaeda sleeper agent.
Charkaoui's religious studies classes were suspended after authorities revealed that the students had traveled to Syria.
A school official would not confirm whether the students were enrolled there.