Background Understanding the long-term psychosocial impact of pediatric hematopoietic stem cell transplantation (HSCT) for non-malignant diseases is needed in order to optimize pre-HSCT counseling, supportive care, and long-term follow up programs after HSCT for this group of patients and caregivers. Procedure This qualitative study included 14 patients transplanted for a non-malignant disease during childhood. In-depth interviews were held online to explore patients’ perspectives on the long-term psychosocial impact of HSCT on their lives. Results were analyzed based on the Grounded Theory approach. Results Patients’ median age at the time of interview was 19 years (range 14-49) and median years after HSCT was 12 years (range 3-33). Four main themes were identified: (1) Doing okay, (2) Experiencing persistent involvement with healthcare services, (3) Influence on relationships with loved ones, and (4) Impact on patient’s life course. Subthemes extracted were doing okay, feeling of being cured, health limitations, sense of vulnerability, ongoing connection to the hospital, acceptance, friendship, family relations, development of own identity, not taking life for granted, social development, impact on (school) career, and thinking about the future. Conclusions Patients reported active coping strategies and resilience after this high-impact treatment. The data highlight the need for patient-adjusted supportive care, indicating more need of supportive care in the long-term outpatient clinic.