The move towards universal health coverage is premised on having well-functioning health systems, which can assure provision of the essential health and related services people need. Efforts to define ways to assess functionality of health systems have however varied, with many not translating into concrete policy action and influence on system development. We present an approach to provide countries with information on the functionality of their systems in a manner that will facilitate movement towards universal health coverage. We conceptualise functionality of a health system as being a construct of four capacities: access to, quality of, demand for essential services and its resilience to external shocks. We test and confirm the validity of these capacities as appropriate measures of system functionality. We thus provide results for functionality of the 47 countries of the WHO African Region based on this. The functionality of health systems ranges from 34.4 to 75.8 on a 0–100 scale. Access to essential services represents the lowest capacity in most countries of the region, specifically due to poor physical access to services. Funding levels from public and out-of-pocket sources represent the strongest predictors of system functionality, compared with other sources. By focusing on the assessment on the capacities that define system functionality, each country has concrete information on where it needs to focus, in order to improve the functionality of its health system to enable it respond to current needs including achieving universal health coverage, while responding to shocks from challenges such as the 2019 coronavirus disease. This systematic and replicable approach for assessing health system functionality can provide the guidance needed for investing in country health systems to attain universal health coverage goals.