Khalifa was born in 1948 in Jarabulus, Syria. He spent his childhood in Aleppo, where he began participating in political activities as a teenager. For this reason, he was arrested and imprisoned twice. After his release, Khalifa studied art and film directing in France and was arrested at Damascus airport upon his return from Paris. From 1982 to 1994, Khalifa was detained without trial in various State Security prisons, including the notorious Tadmor prison. The National Academy of Sciences reported that he was imprisoned on suspicion of membership in the banned Communist Action Party, while according to other sources, his arrest was on charges of membership in the Muslim Brotherhood, stemming from a report written by a fellow student abroad.