"Canadian Ambassador Troy (Lulashnyk) kindly escorted me to the gate at Cairo airport. A glorious end to our battle for freedom!" he tweeted.
An airport security official confirmed that Fahmy had boarded a flight bound for London.
Fahmy, along with colleagues Baher Mohamed and Peter Greste who was deported at the beginning of the year, were convicted in an August retrial of fabricating "false" news in support of the banned Muslim Brotherhood.
President Abdel Fattah al-Sisi pardoned Fahmy, Mohamed and 100 other prisoners last month.
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The status of Greste, an Australian, is still unclear.
After his release, Fahmy said: "I'm feeling ecstatic knowing that I don't have to worry about lawyers, police officers following me all over the place and knowing that I'm going to share my apartment tonight with my beloved wife.
"Now we're free, me and Marwa are going to celebrate. We're going to go back to Canada and travel and... Get on with our lives."
The case sparked global criticism of Sisi, who has said he wished the journalists had been deported from the outset.
Their arrest in December 2013 came at a time of heightened unrest and a deadly crackdown on the Brotherhood following Islamist president Mohamed Morsi's overthrow by the military.
At the time, Qatar, which owns Al-Jazeera, had been supportive of the Islamists.