Joshua Boyle was freed last October along with his American wife Caitlan Coleman and their three children born in captivity.
The identity of the alleged victim was being withheld by a court, according to Boyle's lawyer Eric Granger.
Granger added his client was "presumed innocent" and had never been in any form of legal trouble before.
"We look forward to receiving the evidence and defending him against these charges," he said, adding Boyle would appear before a court in Ottawa on Wednesday.
In a statement to The Toronto Star and published on the newspaper's website, Boyle's wife would not comment on the specific charges "but I can say that ultimately it is the strain and trauma he was forced to endure for so many years and the effects that that had on his mental state that is most culpable for this."
Coleman added that she and the children were healthy.
Boyle and Coleman, who have been married since 2011, were kidnapped by the Taliban during what they described as a backpacking trip through war-torn Afghanistan in 2012, and were later transferred to the custody of the Haqqani faction, known for its alleged ties to the Pakistani military.
They were freed on October 12, but refused to board a US military plane. Boyle, a Muslim convert and long-time advocate of freed Guantanamo inmate Omar Khadr, cited fears over his background.
Mujahid admitted a baby had died but said it was a result of a natural miscarriage.
A month later Coleman also spoke of a sexual "assault" by two of her captors in an interview with ABC news.
Boyle has been an outspoken advocate for Omar Khadr, a Canadian captured at the age of 15 in 2002 in Afghanistan and held at Guantanamo Bay before being transferred to Canada and later released.
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