Infective endocarditis (IE) is associated with high mortality. However, data on factors associated with length of stay (LOS) in hospital due to IE are scarce. In addition, long-term mortality of more than 1 year is inadequately known. In this large population-based study we investigated age and sex differences, temporal trends, and factors affecting the LOS in patients with IE and in-hospital, 1-year, 5-year and 10-year mortality of IE. Data on patients (≥18 years of age) admitted to hospital due to IE in Finland during 2005–2014 were collected retrospectively from nationwide obligatory registries. We included 2166 patients in our study. Of the patients 67.8% were men. Women were older than men (mean age 63.3 vs. 59.5, p<0.001). The median LOS was 20.0 days in men and 18.0 in women, p = 0.015. In the youngest patients (18–39 years) the median LOS was significantly longer than in the oldest patients (≥80 years) (24.0 vs. 16.0 days, p = 0.014). In-hospital mortality was 10% with no difference between men and women. Mortality was 22.7% at 1 year whereas 5- and 10-year mortality was 37.5% and 48.5%, respectively. The 5-year and 10-year mortality was higher in women (HR 1.18, p = 0.034; HR 1.18, p = 0.021). Both in-hospital and long-term mortality increased significantly with aging and comorbidity burden. Both mortality and LOS remained stable over the study period. In conclusion, men had longer hospital stays due to IE compared to women. The 5- and 10-year mortality was higher in women. The mortality of IE or LOS did not change over time.