To estimate the prevalence and incidence rate of systemic lupus erythematosus (SLE) in Taiwan by using a population-based longitudinal database from 2001 to 2011. We conducted a longitudinal Health Insurance Database (LHID) containing 1,000,000 beneficiaries’ records for calculation of prevalence and incidence rate of SLE from 2001–2011. The overall prevalence of SLE in Taiwan in 2011 is 8.11 per 10,000 people with 14.3 per 10,000 people in female and 1.62 per 10,000 people in male. The overall incidence rate of SLE is 0.74–1 per 10,000 person-years with 1.09–1.76 per 10,000 person-years in female and 0.12–0.25 per 10,000 person-years in male. The highest prevalence rate was observed at 40–49 age group in females. There were no significant differences in the overall prevalence among the urban, suburban and rural area in Taiwan while the relative risk is higher in male population living in rural area (RR 1.36, 95% C.I. 1.03–1.79, p = 0.0303). The highest income group has a lower relative risk for the prevalence of SLE (RR 0.83, 95% C.I. 0.71–0.97, p = 0.0197). The incidence rate of SLE in male in the rural area is also higher than the urban area (RR 2.34, 95% C.I. 1.3–4.22, p = 0.0046). Our study covers the longest period among the nation-wide population studies of SLE in Taiwan. The prevalence was increasing especially in the elderly.