The Public Health Agency of Canada said in a statement that the baby showed "severe neurological congenital anomalies."
The World Health Organization included the occurence of "congenital malformation associated with a travel-related case of Zika virus infection" in its weekly Zika update.
The WHO did not say where the mother contracted the infection.
This is the second confirmed case of maternal-to-fetal transmission of the virus in Canada. A pregnant woman who was infected while traveling transmitted the virus to her baby, but the child appears to be healthy.
No details on any of the cases were provided in order to protect the privacy of the families.
The total number of confirmed cases of the Zika virus in Canada, meanwhile, has risen to 205 as of August 11.
Two were the result of sexual transmission, while the remainder were travel-related.
Zika often causes no symptoms, but is particularly dangerous for pregnant women because it can lead to the birth defect microcephaly, in which infants are born with unusually small heads and deformed brains.
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