Objective We estimated the incidence of various comorbidities and mortality in a large national cohort of patients with newly diagnosed systemic lupus erythematosus (SLE) compared with matched population comparators. Methods All patients aged ≥18 years with a first-time diagnosis of SLE in the Danish National Patient Register from 1996 to 2018 were included (n=3,178). For each SLE patient, 19 age- and sex-matched population comparators were identified (n=60,090). Comorbidity diagnoses and mortality data were retrieved from national Danish registries. For comorbidities and mortality, incidence rates per 1,000 person-years and age- and sex-adjusted incidence rate ratios (IRRs) were estimated during the following time intervals: year 1, year 2, years 3-5, and years 6-10 following SLE diagnosis. Results 84.3 % of patients with SLE and general population comparators were female; the mean age at baseline was 47.4 years. Patients with SLE had a significantly increased risk of developing comorbidities during follow-up. The highest first-year IRRs were seen for typical features of SLE: coagulopathy, renal disease, and pulmonary embolism. Renal disease, coagulopathy, and osteoporosis had the highest IRRs during the 5-10 years of follow-up. Patients with SLE had 4.1 times increased mortality risk during the first year of follow-up, compared with matched population controls, and 1.6-2.1 times increased mortality risk during subsequent follow-up periods. Conclusion The study provides a comprehensive overview of risk estimates and the timing of comorbidities and mortality in a nationwide cohort of adult SLE patients. These data may be a valuable reference for upcoming works on evaluating comorbidity in SLE.