After the man plunges to his death, other men waiting at the bottom of the building run towards his body and pelt it with stones.
The footage titled 'The Voice of Virtue in Deterring Hell' includes a number of shocking scenes including a beheading, 'Daily Mirror' reports.
Another part of the video, released on April 6 on ISIS terrorist channels, shows a blindfolded man knelt on the floor waiting to be beheaded and another prisoner with his arm stretched out on a table as militants prepare to cut his hand off.
The video, believed to be shot in Syria, then cuts to ISIS fighters destroying and burning Christian relics and pulling a cross down off the top of a church as well as destroying bottles of alcohol.
The professionally shot, edited and produced video cuts between piles of rocks used for stoning and large crowds gathering for prayer.
The allegedly gay man is thrown from the roof of the building, before another blindfolded and kneeling man is brutally beheaded.
The video then shows the body of the man thrown to his death being stoned by a waiting crowd.
ISIS is known for its brutal treatment of homosexuals and the Syrian Observatory for Human Rights estimates that in January this year alone around 25 gay men were murdered by ISIS.