Staphylococcus argenteus is a new species classified as part of the Staphylococcus aureus-related complex in 2015 and has been recognized to be as pathogenic as S. aureus. We describe the first case of endocarditis caused by S. argenteus. A 51-year-old man presented with chief complaints of fever and headaches. On admission, he showed a slight decrease in consciousness level (Glasgow Coma Scale, E4V4M6). Careful physical examination and imaging revealed a systolic heart murmur, Janeway lesions, and complicating convexity subarachnoid hemorrhage (cSAH) of the left frontal lobe. Ceftriaxone 4 g/day was administered immediately after blood cultures were obtained. The next day, all blood cultures grew Gram-positive cocci, identified as Staphylococcus aureus or Staphylococcus argenteus by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, the version of MALDI-TOF MS used could not distinguish these bacteria. Although we could not find valvular vegetation, he was clinically diagnosed with infective endocarditis according to the modified Duke's criteria. Meropenem 6 g/day and linezolid 1.2 g/day were started to cover S. aureus and methicillin-resistant S. aureus. Finally, ampicillin was selected based on drug susceptibility, and the patient was treated for 8 weeks and recovered without permanent damage. The isolated strain formed white colonies on blood agar plates, characteristic of S. argenteus, and differs from golden colony-forming S. aureus. Genetic analysis revealed the isolated strain as S. argenteus (sequence type 1223). Although distinguishing S. argenteus from S. aureus using routine conventional laboratory tests is difficult, the updated library version of MALDI-TOF MS is useful in identifying S. argenteus. Interestingly, all published cases of infection caused by ST1223 have been reported in Japan. Therefore, the trend of infections from the ST1223 strain should be carefully monitored, particularly in Japan. Further investigation is needed to clarify the epidemiology and clinical characteristics of S. argenteus infection, as there are few studies regarding this pathogen.