Objective The aim of the study is to assess trends in public perceptions of health systems in 27 European Union (EU) member states following the financial crisis (2009–2013), in order to discuss observed changes in the context of the financial crisis.

Design Repeated cross-sectional studies.

Setting 27 EU countries.

Participants EU citizens aged 15 years and older.

Methods The study mainly uses the Eurobarometer Social Climate Survey, conducted annually between 2009 and 2013, thereby analysing 116 706 observations. A multilevel logistic regression was carried out to analyse trends over time and the factors associated with citizens’ perceptions of their healthcare systems.

Results Europeans generally exhibit positive perceptions of their national healthcare systems, 64.0% (95% CI 63.6% to 64.4%). However, we observed a significant drop in positive perceptions in the years following the crisis, especially within countries most affected by the crisis. Concerning fiscal characteristics, wealthier countries and those dedicating higher proportion of their national income to health were more likely to maintain positive perceptions. At the individual level, perceptions of healthcare systems were significantly associated with respondents’ self-perceptions of their social status, financial capacity and overall satisfaction in life.

Conclusions Our finding confirms previous observations that citizens’ perceptions of their healthcare systems may reflect their overall prospects within the broader socioeconomic systems they live in; which have in turn been affected by the financial crisis and the policy measures instituted in response.