Lynne Yelich, Canada's minister of state for Foreign Affairs and Consular, said in a statement Canada "joins the families of Dr. Loubani and Mr. Greyson in welcoming their return to Canada."
Yelich then sent out a message via Twitter saying: "Safe travels #johnandtarek #wheelsup" that linked to the statement.
Other media reported that the pair had boarded a flight to Frankfurt, Germany, early Friday en route to Canada.
Greyson, a Toronto filmmaker, and Loubani, a London, Ont., doctor, had been in the country since their arrest in mid-August. The two were arrested after being caught up in violent anti-government demonstrations in Cairo, but never faced any formal charge.
They say they were detained in harsh conditions and spent most of their time in a cockroach-infested cell with dozens of other inmates.
Greyson and Loubani were suddenly released from prison last weekend, raising hopes that their return to Canada was imminent. At Cairo airport, however, they were not allowed to board a flight to Germany and were told their names were on a no-fly list.
Since then, the men had been living in a Cairo hotel while lawyers pushed for their release.