Record-breaking hot weather (exceptional heatwaves) has been increasingly common worldwide, posing a significant threat to human health. However, little is known about the effect of these exceptional heatwaves on mortality in Europe, especially since the coronavirus disease 2019 (COVID-19) outbreak, which converges with climate change to affect healthcare systems and human lives. We collected mortality data of 967 regions in 30 European countries over the last decade (2014–2023) from the Eurostat. A standard time-series analysis was used to estimate the effect of exceptional heatwaves by quasi-Poisson regression model, including the main effect (effect from heatwave intensity) and the added effect (effect from heatwave duration), on mortality for each region during two periods (before and since the COVID-19 outbreak). We used random effects meta-analysis to pool the mortality risk (i.e., relative risk [RR]) and burden (i.e., attributable fraction [AF]) associated with exceptional heatwaves, at the country level and for Europe as a whole. In Europe, the mortality burden attributable to main and added effects increased from 0.492% (95% CI: 0.488%–0.496%) to 1.276% (95% CI: 1.266%–1.285%) and from 0.307% (95% CI: 0.294%–0.318%) to 0.428% (95% CI: 0.407%–0.448%), respectively. Furthermore, substantial variations across countries were observed, with some countries such as France and Spain experiencing a large increase in the mortality burden attributable to exceptional heatwaves since the COVID-19 outbreak. Our findings underscore the urgent need for heat-health actions to consider the multi-effects of exceptional heatwaves amidst a warming climate.