Background and purpose Stroke is the second largest single cause of death in Europe, responsible for 9% and 13% of all deaths in men and women, respectively. There have been large overall declines in stroke mortality rates in the majority of European countries in recent decades. The aim of this study was to analyse trends in mortality caused by stroke in the 28 member countries of the European Union (EU) over the last two decades. Methods We extracted data for age-standardized stroke mortality rates per 100 000 in the EU for the period 1996-2015 from the World Health Organization database. Joinpoint regression analysis was used to analyse the trends and compute the annual percent change (APC) in the EU as a whole and by country. Analyses were conducted by gender and by European region. Results Mortality from stroke has decreased in the EU over the study period by an average APC of 4.2%. All countries showed downward trends, with the sharpest decreases in Estonia, Portugal and Austria. We recorded statistically significant decreases of 4.2% and 4.3% in mortality rates in men and women, respectively, in the whole EU. Southern and western countries showed the steepest decreases, whereas mortality has increased in northern countries in recent years. Conclusions Stroke mortality has decreased in the EU, in both sexes, especially in southern and western European countries. Our results could be a reference for the development of primary prevention and acute management of stroke policies focused on countries with higher mortality.