Allogeneic hematopoietic stem cell transplantation (allo-HSCT) has become increasingly used as a therapeutic treatment for several pediatric conditions, however the long-term mental health sequelae remain understudied among these survivors. Our objective was to conduct a systematic literature review to determine the association between allo-HSCT and anxiety, depression, and psychological health-related quality of life (HRQOL) in pediatric allo-HSCT recipients compared to survivors of pediatric cancer or healthy children. A literature search of peer-reviewed databases was conducted. Data extraction was conducted using a standardized form. Due to the heterogeneity in studies, populations, and measurement instruments, only a qualitative synthesis was performed. A total of 24 studies met eligibility criteria. Rates of anxiety and depression were higher among survivors of pediatric allo-HSCT compared to population normal values or children treated for health conditions without allo-HSCT. Most allo-HSCT survivors self-reported psychological HRQOL within normal levels, although some studies in leukemia patients identified poorer psychological HRQOL. The presence of multiple chronic health conditions, chronic graft-versus-host-disease, and patient sex were important risk factors for worse mental health. Patients who receive allo-HSCT during childhood experience subsequent anxiety, depression, and poorer psychological HRQOL after transplant and several clinical characteristics contribute to these mental health sequelae.