PurposeThis paper describes distinctive ethical challenges encountered in qualitative research with migrant children. It brings attention to how the exploratory nature of qualitative research, intersected with the multifaced realities of migrant children, shapes stances towards these ethical challenges.Design/methodology/approachThe paper is developed through conceptual and reflective contributions. It narrates distinctiveness within ethical challenges via the literature. It then illustrates these, through the author's experiences of negotiating such tensions on a project with a category of migrant children, namely, separated children.FindingsEthical choices are made throughout the research processes. These choices need to be matched to distinctive childhood and migration intersections, and methodological frameworks must reflect these, including when applied to standardised ethical guidelines. Transparency, reflexivity and positionality influence these choices, and researchers have enhanced responsibility to minimise harm in how they research migrant children.Research limitations/implicationsFindings relate to work in development, where sensitivities regarding research conduct are still present. The scope is therefore on particular challenges of dealing with ethical codes and practices. The intention of the author is for this to be a reflective discussion producing paper, but not a practice guide.Originality/valueIts value is centred on taking generalised ethical challenges in qualitative work with children and systematically contextualising these regarding factors specific to migrant children, arguing that the way which migrant children are represented is in itself a key ethical challenge. It further contributes to the body of knowledge by describing procedures of a qualitative study which address some of this distinctiveness.