The Russian-supervised evacuation of Waer was agreed earlier this month and is expected to last several weeks.
The new agreement aims to finalise implementation of a "reconciliation deal" that has already seen several phases of rebel evacuation from Waer district, but which had stalled in recent months.
Russian troops and vehicles could be seen on Saturday morning just outside the Waer district as the first buses began to pull out, AFP's correspondent said.
The first wave of three green buses pulled out of Waer carrying dozens of fighters, their rifles slung over their soldiers, and civilians including children.
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Between 400 and 500 people are expected to leave today, Syrian state television reported.
Rebels will be bussed to opposition-held parts of Homs province, the town of Jarabulus on the Syrian-Turkish border or the northwest province of Idlib.
The Syrian Observatory for Human Rights monitoring group estimates that a total of 12,000 people, including 2,500 rebels, will leave under the deal.
But the opposition says it is forced into such deals by siege and bombardment.
Three waves of rebels and their families have already quit Waer under an agreement first reached in December 2015, but the deal has stalled since then.
Over the past month, government forces have stepped up bombardment of the district, killing dozens of people, according to the Britain-based Observatory.
And no aid has reached the area in at least four months, with a UN convoy that attempted to reach Waer in February seized by gunmen who diverted the assistance to a government-held area.
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