The video shows the two men apparently being shot dead by the child after being interrogated on camera about their alleged attempts to infiltrate IS in Syria.
Entitled "Uncovering an Enemy Within" in English, the video is narrated in Russian and opens with the interrogation of one of the men, who says he is a Kazakh citizen.
He says he was recruited by Russia's Federal Security Service (FSB) to get close to an unnamed IS fighter.
The second man, who does not give his nationality but says he worked for the FSB in Russia previously, says he was tasked with killing an unnamed IS fighter.
Both men say they were told to collect and transmit information about IS fighters in Syria.
After the interrogations, the video cuts to an outdoors scene, where a bearded adult IS fighter in military-style clothes is standing next to a young boy armed with a pistol.
The man recites religious verses and says the two men are in the "custody of the lion cubs" of IS's self-declared Islamic "caliphate".
The boy has long hair and is dressed in a black zip-up sweater and military-style trousers.
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The two men, dressed in matching grey outfits, are kneeling before the man and the child, who steps forward and shoots both men once in the head and then several times again after they collapse.
The end of the video appears to feature footage of the same boy from an earlier IS propaganda video telling an interviewer he wants to grow up to kill "infidels".
That footage appears to come from a video that emerged last year, showing the boy participating in a training camp for children, taking apart and reassembling a gun.
In that video, he gave his name as Abdallah, and said he was from Kazakhstan.
Russia's FSB agency had no immediate comment on the video.
The video appears to be the first time IS has shown a child carrying out an execution, though it has regularly featured children in its footage, showing them watching grisly killings and training to fight.
IS has held multiple foreign hostages, including a number of Western journalists and aid workers, beheading five of them in gruesome videos published online.
The group, which emerged from Al-Qaeda's one-time Iraq affiliate but has since split with the organisation, controls swathes of territory in Syria and Iraq.
It has declared an Islamic "caliphate" in territory it holds and has been accused of abuses ranging from slavery to forms of crucifixion.