The pill, also known as RU-486, is already legal in 60 countries, including the United States and France, where it was legalized in 1988.
Unlike the morning after pill, mifepristone can be taken up to seven weeks after conception to terminate a pregnancy, depending on national laws.
It allows women to terminate unwanted pregnancies without undergoing surgery.
The drug will be marketed under the name Mifegymiso, and was approved after a period of review that opened in 2012.
"The decision to authorize Mifegymiso for the Canadian market was made further to a thorough review of the data package provided by the sponsor that supported the safety, efficacy and quality of the product," Health Canada said in a statement.
More From This Section
"The approval of mifepristone is great news for women in Canada," the group's president Vicki Saporta said.
"It's long overdue that Canadian women also have access to the gold standard for medical abortion care."
Mifepristone is expected to become available in early 2016, according to NAF.
Doctors in Canada will be permitted to prescribe the drug up to seven weeks after conception, according to records from Health Canada's review.
Drug manufacturer Linepharma International had requested Health Canada to make the drug available.