Bhutan’s education system has made significant strides in terms of access and infrastructure development. Nevertheless, enhancing the quality of learning continues to pose a persistent challenge, despite the implementation of the Education Management Information System (EMIS) to monitor factors that impact learning quality. This study evaluates the effectiveness of Bhutan’s Education Management Information System (EMIS) and the Motherboard platform using the Systems Approach for Better Education Results (SABER-EMIS) framework. Drawing on a cross-sectional evaluative design and a cross-sectional survey of 281 schools, 20 district education officers, and national-level stakeholders, the study identifies discrepancies between intended system design and operational performance. The findings are synthesized into a four-domain evaluation framework encompassing (a) enabling environment, (b) system soundness, (c) data quality, and (d) data utilization in decision-making. Results indicate that while data quality and utilization are approaching established levels, enabling conditions and system integration remain at emerging stages, constraining the effectiveness of data-driven educational management. The study contributes a transferable evaluation model for assessing EMIS effectiveness and highlights the value of integrating quantitative administrative data with qualitative learning analytics. Based on the findings, the paper proposes a phased roadmap combining short-term improvements in data validation and accessibility with long-term strategies for interoperability, capacity development, and international benchmarking. The framework and findings offer practical and scalable insights for strengthening education data systems in low- and middle-income contexts.