The father claims the boy’s mother was “one of the world’s most wanted terrorists”, Sally Jones, according to RT online.
The man, who asked to remain nameless for safety reasons, said he was shocked to see his son in the Islamic State video.
He and Sally Jones, a 47-year-old mother of two, split soon after Jojo was born in Kent in 2004.
Sally Jones then converted to Islam, married computer hacker Junaid Hussain and relocated to Syria in 2013 along with a then-10-year-old Jojo.
It was believed her husband died in a drone strike last year, reported the Mail on Sunday.
In the video released on Saturday, five boys of similar age, all dressed in army clothing, line up behind a row of Kurdish captives in orange jumpsuits.
The boy thought to be Jojo was referred to in the footage as Abdullah al-Britani (Briton) while the other boys seemingly hail from Tunisia, Egypt, Turkey and Uzbekistan.
“He was brilliant, just a normal boy – always chasing bugs, going down the park… It’s disgusting he’s been brainwashed,” said the boy’s father in an interview.