Homs, in central Syria, was once dubbed the "capital of the revolution" and saw some of the first protests against President Bashar al-Assad, in 2011.
The first bus has left the rebel-held area of Al Waer in Homs, the Syrian Observatory for Human Rights said. About 800 people, including rebel fighters and civilians are due to leave throughout Wednesday, the observatory said.
Under the UN-backed ceasefire, food aid has reached the neighbourhood for the first time in nearly a year. Anti-government protests erupted in Homs, Syria`s third-largest city, in 2011.
Soon, thousands of Homs residents were taking part in demonstrations despite a brutal crackdown by security forces and pro-Assad militiamen that left dozens dead.
But in 2012 the Syrian military began a major operation to retake the city, bombarding rebel-held areas.
This very sensitive and significant deal has been reached after more than two years of sporadic negotiations.
Under the first phase of the agreement, hundreds of fighters, including those linked to al-Qaeda, will leave the besieged neighbourhood.
More moderate groups who have accepted the ceasefire will remain in al-Waer for the moment. Syrian activists criticise such deals as surrenders forced by punishing blockades.
But the Syrian government, which has concluded similar deals in other areas, sees them as the best way to end the fighting on its own terms.
And in some areas they have allowed some groups to keep their weapons and some control over their own communities.
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