Background: Through the last two decades the prevention, diagnosis and treatment of pulmonary embolism (PE) has evolved along with demographic changes. The influence of these current transformations is important in the assessment of the future burden of PE. We aimed to describe age specific temporal trends in incidence of first-time PE and subsequent mortality. Methods: We identified patients ≥18 years of age with a first-time in-hospital diagnosis of PE in Danish national registers. By dividing patients into seven age groups (18–34, 35–44, 45–54, 55–65, 65–74, 75–84, >85 years), age specific incidence and 1-year mortality rates were calculated for four different calendar periods between 1999 and 2018. Results: From 1999 to 2018 65,478 patients with a first-time PE were identified. PE incidence per 100,000 person years increased during the study period in all age-groups (18–34 years: 10 to 18, 35–44 years: 18 to 35, 45–54: 26 to 63, 55–64 years: 42 to 123, 65–74 years: 92 to 229, 75–84 years: 166 to 383 and >85 years: 155 to 417), p_trend <0.0001 for all. During the study period 1-year mortality rate decreased from 4 to 2 per 10 person years in patients aged 65–74 years and this trend was found in all age groups (p_trend = 0.0001 for all). Conclusion: Despite a decreasing mortality rate, incidence rate of PE increased in Denmark across all age groups from 1999 to 2018, reflecting improved sensitivity of diagnostic methods and changes in the burden of comorbid conditions, all together warranting a continuing need for early prevention of PE.