Background Little updated population-based evidence exists of temporal trends in infective endocarditis (IE). Methods For the 1994–2011 period, we used Danish nationwide registries to identify cases with first-time IE and to estimate the population size. We calculated the incidence rate of IE in 3-year intervals. To evaluate time trends in incidence, we used the 1994–1996 period as reference and computed incidence ratios and 95% confidence intervals (CI) as the incidence in each of the subsequent 3-year intervals divided by the incidence in the reference period. Results We identified 5486 incident IE patients (65% men) and the mean age at diagnosis was 63 years. Men tended to be younger at diagnosis than women; 62 years vs. 65 years. Mean age at IE diagnosis steadily increased from 57 years in 1994–1996 to 65 years in 2009–2011. The IE incidence rate increased from 3.93 per 100,000 person-years in 1994–1996 to 7.55 per 100,000 person-years in 2009–2011, corresponding to an incidence ratio of 1.92 (95% CI: 1.74–2.12). The increase in incidence over time was more pronounced in men (2.28, 95% CI: 2.02–2.59) than in women (1.39, 95% CI: 1.18–1.64). We observed no increase in incidence over time for subjects younger than 50 years, whereas the incidence increased substantially over time for elderly patients, with the highest incidence ratio of 3.38 (95% CI: 2.55–4.52) for patients more than 80 years at IE onset. Conclusion The incidence of IE increased over time particularly among men and for the older age groups.