The 15-year-old victim was sentenced to death after he was tried by an Islamic court in Deir ezzor.
According to Islamic State’s radical interpretation of Sharia law, homosexuality is considered an offence punishable by death.
A witness said the execution took place in public, in front of a large gathering of local civilians in the area.
Despite condemning the victim to death, the ISIS militant who reportedly raped him was only demoted and spared the death sentence.
Media activist Sarai al-Din said: “The boy was accused of being engaged in a homosexual relation with the prominent ISIS officer.
“[The ISIS militant leader] was forced to leave Syria and join the fighting fronts in northwestern Iraq.
“The decision has been taken by the ISIS leadership.”