Purpose The purpose of the study was to investigate the usefulness of quantitative salivary single-photon emission computed tomography/computed tomography (SPECT/CT) using Tc-99m pertechnetate in Sjögren's syndrome (SS). Methods We retrospectively reviewed quantitative salivary SPECT/CT data from 95 xerostomic patients who were classified as either SS (n = 47, male:female = 0:47, age = 54.60 ± 13.16 y [mean ± SD]) or non-SS (n = 48, male:female = 5:43, age = 54.94 ± 14.04 y) by combination of anti-SSA/Ro antibody, labial salivary gland biopsy, unstimulated whole saliva flow rate, and Schirmer's test. Thyroid cancer patients (n = 43, male:female = 19:24, age = 46.37 ± 12.13 y) before radioactive iodine therapy served as negative controls. Quantitative SPECT/CT was performed pre-stimulatory 20 min and post-stimulatory 40 min after injection of Tc-99m pertechnetate (15 mCi). The %injected dose at 20 min and the %excretion between 20 and 40 min were calculated for parotid and submandibular glands, generating four quantitative parameters: %parotid uptake (%PU), %submandibular uptake (%SU), %parotid excretion (%PE), and %submandibular excretion (%SE). The most useful parameter for SS diagnosis was investigated. Results The uptake parameters (%PU and %SU) were significantly different among the SS, non-SS, and negative controls (p = 0.005 for %PU and p < 0.001 for %SU, respectively), but the excretion parameters (%PE and %SE) were not (p > 0.05 for both). The %PU and %SU were significantly lower in SS than in the negative controls and non-SS (p < 0.05 for all pair-wise comparisons). Additionally, the %SU was significantly lower in non-SS than in the negative controls (p < 0.05). Receiver-operating characteristic analysis revealed that the %SU had the greatest area-under-the curve of 0.720 (95% confidence interval = 0.618-0.807). Using the optimal cutoff value of %SU ≤ 0.07%, SS was identified with a sensitivity of 70.21% and a specificity of 70.83%. Conclusion Reduced submandibular uptake of Tc-99m pertechnetate at 20 min (%SU) was proved useful for the diagnosis of SS. Quantitative salivary gland SPECT/CT holds promise as an objective imaging modality for assessment of salivary dysfunction and may facilitate accurate classification of SS.