•Stenotrophomonas maltophilia is a Gram negative, low virulence, one of the leading multiple-drug-resistant pathogen and quite often causes nosocomial infection.•Bacteremia with Stenotrophomonas maltophilia has higher mortality than Pseudomonas aeruginosa.•Stenotrophomonas maltophilia endocarditis is too scarce, however, it accompanied with high rates of mortality and morbidity.•Acute bacterial endocarditis due to Stenotrophomonas maltophilia can occur even in patients with uncorrected congenital heart disease and lack of immune deficiency, therefore. clinicians should be aware.