To investigate the risks of overactive bladder (OAB) and bladder pain syndrome/interstitial cystitis (BPS/IC) in primary Sjögren’s syndrome (pSS) patients. A nationwide, population-based cohort study was conducted using data from Taiwan’s National Health Insurance Research Database. From 2001 to 2010, participants with newly diagnosed pSS were recognized as the study group. In addition, a comparison cohort of non-pSS participants was matched for age, gender, and initial diagnosis date. Risks of developing OAB and BPS/IC in pSS patients of different age, sex, and various therapeutic strategies were calculated. Hazard ratios (HR) and a 95% confidence interval (CI) were analyzed by Cox proportional hazard model. In total, 11,526 pSS patients were recognized. The HRs of OAB and BPS/IC in pSS patients were 1.68 (95% C.I.: 1.48–1.91, p<0.01) and 2.34 (95% C.I.: 1.59–3.44, p<0.01), respectively. The risks of OAB and BPS/IC were significantly increased for pSS patients aged < 65 years (HR: 1.73 and 2.67), female patients (HR: 1.74 and 2.34), and patients requiring treatment for dry eyes and dry mouth (HR: 2.06 and 2.93). pSS patients exhibited an increased risk of OAB and BPS/IC. Female gender, younger age, and severe glandular dysfunction requiring treatments were potential risk factors.