As part of the deal, government forces are allowing thousands of rebels and civilians to leave two towns in southwest Syria: Madaya and Zabadani, according to the London-based Syrian Observatory for Human Rights.
The Syrian Observatory for Human Rights said 98 evacuees from the northern towns of Fuaa and Kafraya were killed when an explosives-laden vehicle hit their buses at a transit point west of Aleppo on Saturday.
Graphic images circulated over social media showed several bodies, body parts and blood scattered on the ground among mangled buses.
There was no immediate claim of responsibility for the bombing, though the key Ahrar al-Sham rebel group denied any involvement.
Fuaa and Kafraya have been under rebel siege for more than two years.
The BBC reported that he wished that the god may sustain the efforts of those who were bringing healing and comfort to the people of Syria.
UN Secretary General Antonio Guterres condemned the bombing and called on all parties "to ensure the safety and security of those waiting to be evacuated".
The agreement had stalled, leaving thousands of people from both government-besieged and rebel-besieged areas stranded at two transit points on the city's outskirts, before the explosion occurred.
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It added that the Saturday bombing complemented the U.S. attack on the Shayrat Airfield in Homs Province with a barrage of 59 Tomahawk missiles on April 7, which caused some 15 fatalities, including civilians.
Syrian children, wounded in a suicide auto bombing that targeted their buses in Rashidin, west of Aleppo on April 15. Last month, the United Nations described the situation in the pro-government north-western towns of Foah and Kefraya, and the rebel-held towns of Madaya and Zabadani near Damascus, as "catastrophic".
A bus sits damaged after the attack outside Aleppo, Syria at the weekend. There were fears of revenge attacks on evacuees from rebel-held towns, being moved under a deal. At least 70 people, including a number of young children, died in a toxic gas attack earlier this month in the town of Khan Sheikhoun.
Madaya and Zabadani have been under the control of anti-government fighters but facing siege from forces loyal to the regime.
Residents of Madaya and Zabadani joined the 2011 uprising against Assad.
Foua and Kfraya, besieged by the rebels, lived under a steady hail of rockets and mortars.
The evacuees from Madaya headed to rebel-held Idlib, west of Aleppo.
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