Non-communicable diseases represent 71% of all deaths worldwide. In 2015, Sustainable Development Goals, including target 3.4 of SDGs, were seated on the world agenda; “By 2030, reduce premature mortality from NCDs by one-third. More than half of the world’s countries are not on track to reach SDG 3.4, and the COVID-19 crisis has hampered the delivery of essential NCD services globally, which means the premature death of millions of people and indicates the need for capacity building for health systems. We designed a tool to measure the capacity of the National Center for Non-Communicable Disease and then presented the proposed policy package to enhance the national center’s organizational capacity. The data for this explanatory sequential mixed method study was collected using quantitative and qualitative approaches between February 2020 and December 2021. The tool for assessing organizational capacity for NCDs was developed, and its validity and reliability were measured. The developed tool assessed the organizational capacity by evaluating NCNCD’s managers and experts. Following the quantitative phase, a qualitative phase focused on the low-capacity points revealed by the tool. The causes of low capacity were investigated, as well as potential interventions to improve capacity. The developed tool comprises six main domains and eighteen subdomains, including (Governance, Organizational Management, Human Resources Management, Financial Management, Program Management, and Relations Management) which verified validity and reliability. In seven separate National Center for Non-Communicable Disease units, the organizational capacity was measured using the designed tool. (Cardiovascular disease and hypertension; diabetes; chronic respiratory disease; obesity and physical activity; tobacco and alcohol; nutrition; and cancers). The organizational management dimensions and the sub-dimensions of the organizational structure of the Ministry of Health and Medical Education and units affiliated with the national center, in all cases, were almost one of the main challenges that affected the country’s capacity to fight against NCDs. However, all units had a relatively good situation in terms of governance (mission statement, vision, and written strategic plan). The content analysis of experts’ opinions on the low-capacity subdomains highlighted challenges and recommended capacity-building interventions. Transparency in methods and processes is necessary to allocate funding among various health programs and evaluate their effects through cost-effectiveness indicators. This study identified weak points or areas where capacity building is required. The root causes of low capacity and interventions to build capacity are listed in each dimension of the tool. Some of the proposed interventions, such as strengthening organizational structures, have the potential to impact other domains. Improving organizational capacity for NCDs can assist countries to achieve national and global goals with greater efficiency.