The drone which is known as a General Atomics MQ-9 Reaper, capable of remotely controlled or autonomous flight operations, spotted the group of jihadists mustering a large crowd in the town of Abu Kamal in eastern Syria.
"Given the large number of civilians present, the Reaper's crew could not target directly the Daesh fighters about to carry out the murders," a MoD spokesperson said in a recent statement.
"However, two armed extremists were stationed as sentries on the roof of a building overlooking the scene," the spokesperson added.
The MoD subsequently released a Hellfire missile that was fired immediately and directly hit one of the sentries and brought the execution to an immediate halt.
The attack itself took place on May 9.
Between December 2015 and December 2016, the RAF launched 73 airstrikes over Syria, killing an estimated 120 Daesh fighters and injuring a further 12.