"Coordinated with our coalition partners, two CF-18s attacked ISIL targets with GBU12 500-pound (227-kilogram) laser-guided bombs in the vicinity of Fallujah," Defense Minister Rob Nicholson said in a statement.
"All aircraft returned safely to their base."
Nicholson declined to detail damage caused to the targets during the approximately four-hour mission, indicating that such details would be provided during a news conference Tuesday.
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Canada conducted its first airstrikes in the anti-IS fight following two days of reconnaissance after joining the coalition on Thursday.
"Today's strike demonstrates our government's firm resolve to tackle the threat of terrorism and to stand with our allies against ISIL's atrocities against innocent women, children and men," Nicholson said, using another acronym by which IS is known.
"I thank all our men and women in uniform for their work on this important mission."
In Syria, coalition aircraft hit IS positions in five separate strikes near the border town of Kobane over the weekend. The strikes struck five small IS units and destroyed three IS vehicles, according to US Central Command.
The Canadian strikes came as French President Francois Hollande visited Canada. He was expected to discuss the conflict in Iraq with Canadian Prime Minister Stephen Harper.