The Church was canonically instituted by Pope Shenouda III on July 2, 1974, as the French Coptic Orthodox Eparchy. On June 18, 1994, Pope Shenouda raised the status of the Eparchy to the French Coptic Orthodox Church, a new, self-governing body (the church is integrated within the Church of Alexandria, but is considered autonomous in matters of governance).
The church was headed by Metropolitan Marcos until his death on May 11, 2008. The seat of the head of the French Coptic Orthodox Church remained vacant until the enthronement of Bishop Athanasius, a member of the Holy Synod of the Coptic Orthodox Church, to the diocese on June 16, 2013. The French-speaking Coptic community is now served by Bishop Athanasius.