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School refusal (SR) is commonly associated with somatic symptoms that are temporally related to school attendance. Abdominal pain, headache, vomiting, and musculoskeletal pain are frequently encountered and are usually not caused by a physical disease. School refusers, parents and health care workers are often puzzled by these impairing symptoms. In this qualitative study, we assessed somatic symptoms in a population encompassing both school refusers and their parents. We aimed at better understanding experiences and strategies in the management of these debilitating symptoms, while also investigating the journey of these symptoms and their behavioral consequences on the said population. We conducted qualitative interviews both within an Integrated Youth Health Care Unit in Paris and through a French parent-led support group improving care for school refusers. We interviewed 19 young persons with SR (aged 6–21 years old) and 20 parents. Using the Grounded Theory, three themes were identified: (1) somatic symptoms’ journey in four phases (emergence, coping, crisis, and disappearance in the context of school dropout); (2) their deconstruction, indicating the patients’ emotional state; and (3) their management through self-care practices as well as increased emotional and body awareness. Some parents, who could portray similar symptoms at a younger age, mentioned familial pattern of heightened emotional and sensorial sensitivity as a possible cause. Findings suggested that somatic symptoms in SR offer an insight into the patients’ emotional state. We recommend that psychotherapies targeting somatic symptoms could be further assessed in SR, along with educational content aimed at increasing emotional literacy in schools and health care settings.