Staphylococcus aureus bloodstream infection (SA-BSI) is an infection with increasing morbidity and mortality. Concomitant Staphylococcus aureus bacteriuria (SABU) frequently occurs in patients with SA-BSI. It is considered as either a sign of exacerbation of SA-BSI or a primary source in terms of urosepsis. The clinical implications are still under investigation. In this study, we investigated the role of SABU in patients with SA-BSI and its effect on the patients' mortality. We performed a retrospective cohort study that included all patients in our university hospital (Charité Universitätsmedizin Berlin) between 1 January 2014 and 31 March 2017. We included all patients with positive blood cultures for Staphylococcus aureus who had a urine culture 48 h before or after the first positive blood culture. We identified cases while using the microbiology database and collected additional demographic and clinical parameters, retrospectively, from patient files and charts. We conducted univariate analyses and multivariable Cox regression analysis to evaluate the risk factors for in-hospital mortality. 202 patients met the eligibility criteria. Overall, 55 patients (27.5%) died during their hospital stay. Cox regression showed SABU (OR 2.3), Pitt Bacteremia Score (OR 1.2), as well as moderate to severe liver disease (OR 2.1) to be independent risk factors for in-hospital mortality. Our data indicates that SABU in patients with concurrent SA-BSI is a prognostic marker for in-hospital death. Further studies are needed for evaluating implications for therapeutic optimization.