Background: The association between mortality and heatwaves is well documented. Heatwaves frequency, intensity, and duration increase with global climate change. The most vulnerable group for dying during heatwaves is older people. Knowing which diseases contribute to a higher number of deaths during heatwaves is important for planning appropriate public health preventive measures. Methods: We assessed the short-term association between the number of deaths for older adults (75+ years) and heatwaves in the years 1999 to 2020 in Slovenia. We estimated the relative risks (RR) with a 95% confidence interval for the number of deaths for the observed diagnosis (all causes, circulatory, respiratory) and urban vs. rural areas associated with heatwaves in Slovenia for each year, comparing the number of deaths during heatwaves with reference days. Results: Most years showed no significant increase in deaths during heatwaves for those aged 75 and older. However, in 2006, 2007, 2014, and 2015, there was a significant increase in deaths during heatwaves. For the general population, heatwaves were associated with an increase in deaths due to all causes: 10% more in 2006 and 26% more in both 2007 and 2014. For those aged 75 and older, heatwaves were associated with an increase in deaths due to all causes: 22% more in 2007, 27% more in 2014, and 28% more in 2015. For those aged 75 and older, heatwaves were associated with an increase in deaths due to circulatory system diseases: 25% more in 2006, 33% more in 2007, 30% more in 2014, and 27% more in 2015. Regarding urban vs. rural areas, in 2006 and 2012, the elderly in urban areas were more affected, with 33% and 26% more deaths, respectively. In contrast, in 2007, 2014, and 2015, old age population in rural areas was more affected, with 29%, 26%, and 31% more deaths, respectively. Conclusions: According to the literature data, older adults are most susceptible to the effects of extreme heat due to physiological changes that occur with aging, chronic diseases, certain medications, a sedentary lifestyle, and social isolation. The results of our study will help in planning appropriate preventive public health measures to better protect older adults during the next heatwaves in Slovenia.