The United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) was one of the earliest healthcare systems globally to implement the International Classification of Diseases, Eleventh Revision (ICD-11) across its 140 clinics serving 5.9 million Palestine refugees. This paper discusses the integration of ICD-11 into UNRWA's cloud-based electronic medical record (EMR) system, identifying both the barriers and facilitators involved and analyzing trends in clinical documentation and healthcare utilization. The key challenges included data privacy provisions, integration into a coordinated care model, complex classification schema for primary care settings, frequent staff turnover, and limited data analysis capabilities. Conversely, facilitators included physician-tailored training and on-site support, system compatibility, a multidisciplinary team approach, policy support from UNRWA and the World Health Organization (WHO), and leadership commitment and effective change management. Medical officers (MOs) using ICD-11 reported greater satisfaction with the system's capabilities in managing and visualizing health information. This article contributes to the discourse on health data management in complex humanitarian settings, offering insights into the benefits and challenges of implementing advanced classification systems like ICD-11. Future research should explore longitudinal impacts and further integration with global health systems, ensuring that the advancements in classification continue to support the overarching goal of health equity and access in vulnerable and hard-to-reach populations.