Adenosine deaminase (ADA) is essential for immune function, facilitating the conversion of adenosine to inosine. Elevated ADA activity has been observed in several autoimmune disorders, including systemic lupus erythematosus (SLE), which is characterized by the production of autoantibodies and dysregulation of T and B lymphocytes. This study involved thirty-five females diagnosed with SLE disease classified according to the American College of Rheumatology (ACR) criteria and 70 age-matched healthy controls. Blood and saliva samples were collected from all participants both before and after 4 weeks of hydroxychloroquine (HCQ) treatment. Results demonstrated that serum and saliva levels of TADA, ADA1, and ADA2 activities were noticeably higher than those of healthy controls (p < 0.001). During HCQ therapy, the activities of the above enzymes showed a decrease in SLE patients. Although the presence of this decreased, the activities remained high as compared to controls. After treatment, serum and saliva levels of ADA2 activity, which is associated with monocytes and macrophages, were increased significantly compared to controls. In addition, ADA1 activity, which is linked to lymphocyte function, was increased significantly in serum, while in saliva it did not significantly alter as compared to controls. The study highlights the potential of ADA, particularly ADA2, as a biomarker for monitoring disease activity and therapeutic response in SLE. Although HCQ lowers inflammation, ADA levels do not return to baseline, suggesting persistent chronic immunological dysregulation. Salivary ADA as a non-invasive marker for SLE management needs more investigation.