The video shows the boy laying in the back of a truck when a fighter begins to cut off his head with a small knife.
One fighter shouts "we will leave no one in Handarat", which is north of Aleppo city where there has been fighting between rebels and regime forces.
The Britain-based Syrian Observatory for Human Rights confirmed that the video depicts rebel fighters.
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In an earlier clip, the boy was sitting in the back of the truck with fighters around him accusing him with being a member of Al Quds brigade, a Palestinian group fighting with the regime forces.
Earlier in July, Amnesty International issued a report saying that Islamist rebels and jihadists in Syria are guilty of war crimes, accusing them of "a chilling wave of abductions, torture and summary killings".
The London-based rights group named five Syrian anti-regime factions operating in northern Syria among them Nureddin Zinki.
Activists accused Nurredin Zinki group of carrying out the killing, but the group issued a statement condemning a "violation" that was "an individual mistake, that does not represent the general policy of the group".
According to Rami Abdel Rahman, Syrian Observatory for Human Rights chief, "the boy is no more than 13 years old, he was captured Tuesday in Handarat area, but the incident took place in a rebel held area in Aleppo city, Al Mashhad neighbourhood to be exact".
He could not confirm if the boy was a Palestinian or a child soldier, though he said Al Quds brigade denied that he was one of its fighters.
Nureddin Zinki added that "the persons who carried out this violation were arrested and handed over" to a judicial committee for investigation.
Syria's conflict began in 2011 with the repression of anti-government demonstrations and has evolved into a multi-front war that has left more than 280,000 dead and forced millions from their homes.
