The role of hepatitis B virus (HBV) infection in patients with primary Sjögren's syndrome (pSS) remains unclear. Therefore, we investigated the prevalence and clinical significance of HBV infection in Taiwanese patients with pSS. One hundred seventy-five patients with pSS who fulfilled the 2002 American-European Revised Classification Criteria were enrolled. Eighteen (10.3%) patients were positive for hepatitis B surface antigen (HBsAg). There were 4 males and 14 females, with the mean age of 54.4 years. The main immunological feature was rheumatoid factor (13 of 18, 72.2%), which was significantly higher than those negative for HBsAg (28.1%, p < 0.001). Twelve (66.7%) patients developed liver dysfunction, which was significantly different from the 15.3% of patients who were negative for HBsAg (p < 0.001). There was no significant difference in extraglandular features between patients positive and negative for HBsAg, except patients positive for HBsAg had a lower rate to develop pulmonary involvement than those negative for HBsAg (5.6% vs. 29.9%, p = 0.027). The mortality rate of pSS patients positive for HBsAg during follow-up was 12.0% and the presence of HBV infection did not influence the survival rate (p = 0.730). pSS patients with liver cirrhosis presented shorter median overall survival compared to those with without liver cirrhosis (p < 0.001). Our findings suggest that HBV infection may protect individuals from pSS and reduce pulmonary involvement.