Only 40 cases of Stenotrophomonas maltophilia (S. maltophilia) endocarditis have been reported to date, and there is no description in patients with underlying autoimmunity. A 23-year-old woman with systemic lupus erythematosus (SLE) overlapping rheumatoid arthritis (RA) and no risk factors for endocarditis was admitted in our hospital because of community-acquired tricuspid valve endocarditis. During hospitalization, she was complicated with pulmonary thromboembolism and pneumonia. Laboratory showed autoimmune diathesis featured by anti-cyclic citrullinated peptide (anti-CCP), anti-Sm, anti-Ro/SSA, anti-cardiolipin, anti-(β2 glycoprotein 1, and antinuclear antibodies, rheumatoid factor (RF), low complement, lymphopenia and C-reactive protein (CRP) of 425 mg/L. S. maltophilia grew in serial blood culture sets. Empirical broad-spectrum antimicrobials were ineffective until trimethoprim/sulfamethoxazole (TMP/SMX) was added to therapy. One month after admission, the patient underwent successful surgical replacement of the tricuspid valve and the subsequent course was satisfactory, allowing her to be discharged 14 days after. Nowadays, she remains free of complaints and her cardiac, renal and pulmonary functioning is stable. Noteworthy is that all auto-antibodies have been persistently raised over time. Here, we present a compilation of the available information about S. maltophilia endocarditis, and suggest that autoimmunity could be included as a novel predisposing factor for S. maltophilia endocarditis