Background Pediatric hematopoietic stem cell transplantation (HSCT) is a life-saving therapy for malignant and non-malignant hematologic diseases. However, access to this high-complexity treatment remains limited and uneven across the Andean subregion. This study aimed to evaluate the current status, capacity, and equity of pediatric HSCT programs in six Andean countries (Bolivia, Chile, Colombia, Ecuador, Peru, and Venezuela) within the framework of WHO Global Initiative of Childhood Cancer. Methods A mixed-methods, cross-sectional situational assessment was conducted between November 2024 and January 2025 under the coordination of the Andean Health Organization (ORAS-CONHU) and the Pan American Health Organization (PAHO). Standardized national and center-level surveys (34 and 150 items, respectively) were applied to Ministries of Health and HSCT centers to collect data on infrastructure, workforce, financing, quality management, and barriers to access. Quantitative data were analyzed descriptively and validated by national committees, complemented by qualitative interviews with key stakeholders. Results Twenty-seven HSCT centers were identified across the subregion, revealing major disparities in access and capacity. Chile reached 100% coverage of estimated transplant needs, while Colombia, Peru, and Venezuela achieved 80%, 29%, and 42.5%, respectively. Bolivia and Ecuador had the lowest coverage (1.6% and 24%). Only 28% of units were pediatric-exclusive, and less than two-thirds met full quality and training standards. High-cost medicines, limited infrastructure, and shortages of specialized personnel were identified as critical barriers, while regional collaboration and national policies emerged as key facilitators. Conclusion The study highlights significant inequities in pediatric HSCT access and capacity across the Andean subregion. Strengthening infrastructure, workforce training, financing mechanisms, and data systems, supported by sustained regional cooperation, is essential to achieve equitable, high-quality transplant care for all children.