Children undergoing hematopoietic stem cell transplantation (HSCT) are vulnerable to pain due to the intensity and toxicity of this treatment. An instrumental case study design of two qualitative phases was conducted to examine the pain experiences of hospitalized children during HSCT therapy and how contextual factors related to the pediatric HSCT environment influenced their experience of pain. The Social Communication Model of Pain provided the conceptual framework for the study. In Phase 1, semi-structured interviews were conducted with parents of a child undergoing HSCT therapy at two time points. Phase 2 was conducted as a naturalistic observational study of the clinical care provided to children and semi-structured interviews with health-care providers. Children experienced complex and multifaceted pain with physical, psychological, and contextual contributors. Understanding the many factors contributing to the child’s pain experience can inform strategies to improve the management of pain during HSCT therapy.