Although the primary responsibility for health systems within the European Union (EU) lies with its Member States, the EU also has many tools that can support the strengthening of health systems. Many of the EU’s tools can provide support even though strengthening health systems is not their primary objective, such as the European Semester, the Cohesion Policy Funds, Horizon Europe and the Recovery and Resilience Facility. The available tools address different parts of change processes. Making best use of these instruments typically requires combining various EU tools with different objectives across multiple stages of the change process. The need to combine diverse tools creates the challenge for Member States of being aware of many different tools and their potential to support health systems, and in aligning objectives and processes between health objectives and the requirements of those tools. There are some examples of technical assistance from the EU to help with doing this, although none are specifically focused on health systems strengthening. There is potential to combine support from the EU with support from other sources, such as national and regional instruments or other international bodies like the World Health Organization (WHO), although this also presents countries with the challenge of combining instruments with diverse objectives and processes. The EU’s support to health systems respects the primary responsibility of EU countries for their own health systems. Nevertheless, being able to draw on EU support has been increasingly important, in particular for Member States that have joined since 2004, and will become even more vital in the coming years. As health systems across Europe deal with the consequences of the COVID-19 pandemic, there is scope for greater collaboration between individual countries and at EU level to make best use of EU tools to strengthen health systems.