Background: This retrospective cohort study aimed to examine the risk of developing systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) in patients with primary Sjögren’s syndrome (pSS) compared to controls using data from a nationwide health claims database. Methods: Four distinct cohorts of patients with newly diagnosed pSS were established using Taiwan’s National Health Insurance Research Database. Cohorts I and II were created to evaluate the risk of developing SLE and RA, respectively. Cohorts III and IV were assembled similarly to Cohorts I and II but employed a stricter definition, based on catastrophic illness certificate (CIC) status, for identifying patients with pSS. Comparison cohorts of patients without pSS were formed by frequency matching for sex, 5-year age interval, and index year. Incident rate ratios (IRR) for SLE or RA development were determined using Poisson regression models. Results: Patients with pSS, selected from just outpatient visits or with additional CIC status showed a significantly higher risk of developing SLE or RA compared with the controls. When stratified by age group or sex, the risk of developing SLE was notably higher in the young age group (adjusted IRR 47.24,p= 0.002) and women (adjusted IRR 7.63,p= 0.003) among patients with pSS. In addition, both men and women with pSS, irrespective of age, showed a significantly elevated risk of developing RA. Conclusions: Patients with pSS exhibited an elevated risk of developing SLE and RA. Rheumatologists should carefully monitor patients with pSS for potential SLE and RA development.