This case study explores the complex nature of coexisting autoimmune diseases, which is most effectively demonstrated by the coexistence of rheumatoid Arthritis (RA) and systemic lupus erythematosus (SLE), also referred to as “rhupus syndrome.” A comprehensive evaluation of a 28-year-old woman with joint discomfort, morning stiffness, and increased C-reactive protein (CRP) values was conducted. Anti-cyclic citrullinated peptide (CCP), antinuclear antibodies (ANA), and other pertinent serological indicators were examined in the laboratory. The patient’s medical background, prior therapies, and family history were considered to create an individual therapy strategy. The patient’s symptoms remained despite a long history of disease-modifying anti-rheumatic medication (DMARD) use. Positive outcomes for anti-CCP, anti-ANA, and anti-double-stranded DNA (anti-dsDNA) antibodies provide light on the overlap of multiple autoimmune diseases. The diagnostic difficulty was increased when autoimmune neutropenia was diagnosed with a bone marrow biopsy. Once azathioprine therapy was started, symptoms significantly and quickly improved within a month. Azathioprine was found to be successful in the remission of the disease. Azathioprine therapy’s critical role in treating overlapping autoimmune illnesses emphasizes the necessity for individualized and advanced testing and treatment. Targeted immunosuppressive medicines have the potential to make significant advances and enhance patient care and results.