Abstract Background Health systems are not considered to be significantly influenced by European Union (EU) policies given the subsidiarity principle. Yet, recent developments including the patients’ rights and cross-border directive (2011/24 EU), as well as measures taken following the financial crisis, appear to be increasing the EU’s influence on health systems. The aim of this study is to explore how health system Europeanisation is perceived by domestic stakeholders within a small state. Methods A qualitative study was conducted in the Maltese health system using 33 semi-structured interviews. Inductive analysis was carried out with codes and themes being generated from the data. Results EU membership brought significant public health reforms, transformation in the regulation of medicines and development of specialised training for doctors. Health services financing and delivery were primarily unaffected. Stakeholders positively perceived improvements to the policy-making process, networking opportunities and capacity building as important benefits. However, the administrative burden and the EU’s tendency to adopt a ‘one size fits all’ approach posed considerable challenges. The lack of power and visibility for health policy at the EU level is a major disappointment. A strong desire exists for the EU to exercise a more effective role in ensuring access to affordable medicines and preventing non-communicable diseases. However, the EU’s interference with core health system values is strongly resisted. Conclusions Overall domestic stakeholders have a positive outlook regarding their health system Europeanisation experience. Whilst welcoming further policy developments at the EU level, they believe that improved consideration must be given to the specificities of small health systems.