Both atopic diseases and systemic lupus erythematosus (SLE) are immune disorders that may lead to physical complications or multi-system comorbidities. This population-based case-control study was designed to evaluate the risk of SLE associated with atopic diseases. Using a national insurance claims dataset in Taiwan, we identified 1673 patients newly diagnosed with SLE and 6692 randomly selected controls frequency matched for gender, age and index date. The odds ratios (OR) for SLE were calculated for associations with allergic rhinitis, allergic conjunctivitis, atopic dermatitis and asthma. The SLE patients were predominantly female (82.5%) with a mean age of 40.1 (SD = 18.2). The patients with SLE had a higher rate of atopic dermatitis (6.81% vs. 3.06%), and asthma (10.6% vs. 7.64%) was approximately 2 times more common in the patients with lupus than in those without. The patients with atopic disease (atopic dermatitis, allergic rhinitis, allergic conjunctivitis and asthma) were at a significant risk for SLE. The overall risk for SLE increased as the number of atopic diseases increased from 1.46 to 2.29, compared with-individuals without the diseases (p < 0.0001). In conclusion, this population-based case-control study demonstrates a significant relationship between atopic diseases and the risk of SLE, especially for females. Atopic dermatitis plays a stronger role than other types of atopic disease in association with SLE.