But he gave no timeline.
"About an hour ago I spoke with President Obama," Mr Trudeau told a press conference.
While Canada remains "a strong member of the coalition against ISIL," Mr Trudeau said he made clear to the US leader "the commitments I have made around ending the combat mission."
Canada last year deployed CF-18 fighter jets to the region until March 2016, as well as about 70 special forces troops to train Kurds in northern Iraq.
During the campaign, Mr Trudeau pledged to bring home the fighter jets and end its combat mission. But he vowed to keep military trainers in place.
His new Liberal government will be "moving forward with our campaign commitments in a responsible fashion," Mr Trudeau said.
"We want to ensure that the transition is done in an orderly fashion."
The announcement did not feature in a read-out of the phone call released by the White House.
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