Background The involvement of the central nervous system in primary Sjögren syndrome (pSS) remains controversial. Functional magnetic resonance imaging (fMRI) is a relatively new method that can be applied to investigate the heterogeneity of central nervous system (CNS) involvement in pSS patients through regional homogeneity (ReHo) analysis. Purpose To collect data from pSS patients and healthy controls, and use ReHo analysis to elucidate the neurobiological mechanism of CNS involvement in pSS. Material and Methods Fourteen clinically diagnosed pSS patients and 14 age- and gender-matched healthy controls underwent resting-state fMRI. The data were processed by ReHo analysis. The double sample t-test was used to compare ReHo data between groups. Results Compared to controls, pSS patients had significantly increased ReHo values in the right cerebrum, left limbic lobe, right middle temporal gyrus, and the inferior parietal lobe. However, ReHo values significantly decreased in the right lingual gyrus, left cuneiform lobe, left superior occipital gyrus, bilateral middle occipital gyrus, and the fronto-parietal junction area ( P < 0.01, clusters ≥ 50 voxels). Conclusion This study demonstrates the abnormal brain activity in the visual cortex and fronto-parietal junction area in pSS patients, suggesting pathological neuronal dysfunction in these regions.