The aberrant induction of salivary/lacrimal proteins is considered to be crucial in the pathogenesis of sicca-symptoms related to primary Sjögren syndrome (SS). We report the case of an 11-year-old boy who was admitted to hospital due to recurrent bilateral parotid gland enlargement and keratoconjunctivitis, which were diagnosed as primary SS upon a combination of laboratory and instrumental tests. The proteomic analysis of the salivary peptide complex in the patient's salivary fluid near diagnosis and after 6 months of pharmacological therapy revealed quantitative and mostly qualitative differences. This observation reveals that clinical and functional changes of the salivary glands driven by non-steroidal antinflammatory drugs might be reflected in different proteomic patterns of the salivary fluid.