Methicillin-susceptible Staphylococcus aureus (MSSA) clonal complex 398 (CC398) bloodstream infections (BSI) have been increasingly reported and were previously suggested to be associated with increased mortality. We conducted a retrospective cohort study of hospitalised patients with MSSA BSI at Geneva University Hospitals between 2021 and 2023. Among 294 MSSA BSI, 57 (19%) were CC398 and 185 (63%) were healthcare-associated. Crude 90-day all-cause mortality was similar in both groups (19% CC398, 22% non-CC398, p = 0.79). In adjusted analyses, there was no difference in the all-cause mortality hazard between CC398 and non-CC398 patients (aHR 30-day mortality: 0.87, 95%CI:0.41–1.83; aHR 90-day mortality 1.17, 95%CI:0.61–2.25).