There are 1.3 billion people with disabilities globally. On average, they experience greater healthcare needs and more barriers accessing healthcare. Yet, health systems have failed to adequately include people with disabilities. The purpose of this study was to develop and pilot-test a tool for assessing disability inclusion in health system performance. We presented the Missing Billion disability-inclusive health system framework, which includes 4 system-level components and 5 service delivery components, and outputs and outcomes. We developed a tool, consisting of 48 indicators related to the framework components. We consulted international experts, who considered the framework and indicator set to be logical and comprehensive. The tool was pilot-tested in the Maldives (2020) and Zimbabwe (2021), working with local researchers to collect relevant data through document review and key informant interviews. The pilot data demonstrated that collecting data on the indicators was feasible. The tool highlighted areas where the health systems were performing well in terms of disability inclusion (e.g. governance) and other areas where there were large gaps (e.g. leadership) or lack of data (e.g. accessibility, outputs and outcomes). The indicators were updated and refined. We established a process for undertaking the assessment, highlighting the importance of leadership and ownership by the Ministry of Health, to facilitate data collection and implementation of recommendations. In conclusion, this new tool for assessing disability inclusion in health systems performance can help to identify key issues and guide and monitor action.