The video was taken by Israeli human rights group B’Tselem, Euronews informs.
The Israeli army say the boy was throwing stones at soldiers on a street in Hebron in the West Bank.
B’Tselem said the soldiers took the boy home where they met his father and took them both away.
The video shows the child crying and visibly distressed as he is put into the Israeli army truck.
The father and son were held at an army base where the video shows the father bound and blindfolded.
The two were later taken to the Palestinian police who questioned them before releasing them.
While there are criticisms that the detention of the child was illegal, the army argues that the child was posing a threat by throwing stones and that he was not arrested nor were charges laid.