As an end to the humanitarian crisis in the region is not in sight, thousands of children associated or allegedly associated with the Islamic State in Iraq and the Levant (ISIL) remain in displacement and detention camps in Syria and Iraq. Languishing in inhumane conditions and extremely vulnerable to abuse, these children's ongoing suffering calls for urgent action to ensure effective protection and support for reintegration, recovery and education consistent with their needs. Many of these children have ties to other countries since they were born to or raised by parents who had travelled to the conflict zone as so-called ‘foreign fighters’. While the agency of children and the various roles that children have played in ISIL shall not be denied, it is well established that children associated with armed groups should be considered primarily as victims. Still, many states have been hesitant to take responsibility for the repatriation and protection of their underage citizens. However, a failure to address the precarious situation of these children not only appears to be a short-sighted security strategy, but it also denies them of their human rights. Against this background, this contribution provides an overview of some of the main human rights implications related to different repatriation policies and argues for a human rights-based approach, with a central focus on the protection of the rights of the child, to address the challenges related to the return of the children allegedly associated with ISIL.