Background: Functional disorders, defined as disorders with no clear medical explanation, are common and impose a significant burden on youths, their families, healthcare services and society as a whole. Currently, the literature describes resistance among patients and their families towards psychological symptom explanations and treatments. More knowledge about the thoughts and understandings of youths with functional disorders and their parents is needed. The aim of this study was to explore the illness perceptions of youths with severe functional disorders and their parents. Methods: A qualitative interview study using interpretative phenomenological analyses. The study included 11 youths aged 11–15 years with functional disorders and their parents, where interviews were performed at the point of referral from a somatic to a psychiatric treatment setting. Results: Analyses identified three main themes. Themes 1(Ascribing identity to the disorder) and 2 (Monocausal explanations) explore key elements of the participants’ illness perceptions, and theme 3 (Mutable illness perceptions) explores how illness perceptions are influenced by experiences from healthcare encounters. Conclusions: The label ‘functional disorder’ was poorly integrated in the illness perceptions of the youths and their parents. Participants used a monocausal and typically physical explanation rather than a multicausal biopsychosocial explanation for their symptoms.