This population-based study aimed to determine the trend of incidence, prevalence, and mortality of systemic lupus erythematosus (SLE) in a 6-year period in Taiwan. Patients with international classification of diseases ninth revision (ICD-9) code 710.0 were retrieved from the Taiwanese National Health Insurance Research Database (NHIRD), which covered more than 96 % of the entire population, and from the Ministry of Interior between 2003 and 2008 in Taiwan. Patients with SLE registered as catastrophic illness were enrolled for analysis. The incidence rate, prevalence ratio, and mortality rate stratified by sex and age were analyzed. There were a total of 6,675 SLE patients (5,836 females and 839 in males) during the study period. The average annual incidence rate was 4.87 per 100,000 population, and the average female-to-male incidence ratio was 7.15. The ratio increased with age and peaked at the age of 40–49 years, then decreased thereafter. The incidence rate decreased by 4.2 % per year. The highest incidence rate was noted in the 20–29-year-old age group in females and the 70–79-year-old age group in males. The average prevalence and mortality rates were 97.5 and 1.2 per 100,000 population, respectively. Mortality was 3.2 % in patients diagnosed within 1 year and is more prevalent in young patients with average age of 15.6 years. Incidence rate of SLE has been declining in recent years but the prevalence rate has remained steady. The highest mortality rate is among younger patients diagnosed with SLE within 1 year.