Background Data on children who grow up with parents adhering to violent extremism is scant. This makes it extremely delicate to inform policies and clinical services to protect such children from potential physical and psychological harm. Objective This paper explores the predicament of children whose caretakers were referred to a specialized clinical team in Montreal (Canada) because of concerns about risks or actual involvement in violent extremism processes. Methods This paper uses a mixed methods concurrent triangulation design. Quantitative data was obtained through a file review (2016–2020). Qualitative data was collected through semi-structured interviews and a focus group with the team practitioners. Results Clinicians reported the presence of stereotypes in the health and social services network frequently representing religious extremist parents as potentially dangerous or having inappropriate parenting skills while minimizing the perception of risk for parents adhering to political extremism. Children displayed high levels of psychological distress, mainly related to family separation, parental psychopathology, and conflicts of loyalty stemming from familial or social alienation. Conclusions Training practitioners to be aware of their own personal and institutional bias may help them to understand the predicament of extremist parents’ children and implement systemic, trauma and attachment informed interventions.