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Background: <i>Staphylococcus aureus</i> is the main cause of haematogenous prosthetic joint infections (PJI). We aimed to describe the prevalence and factors associated with PJI in patients with documented <i>S. aureus</i> bacteraemia. Methods: Adult patients with <i>S. aureus</i> bacteraemia and presence of prosthetic joint hospitalized in Lausanne University Hospital during a seven-year period (2015–2021) were included. Results: Among 135 patients with <i>S. aureus</i> bacteraemia and prosthetic joints, 38 (28%) had PJI. Multivariate analysis revealed that the presence of PJI was associated with knee arthroplasty (<i>P</i> 0.029; aOR 3.00, 95% CI 1.12–8.05), prior arthroplasty revision (<i>P</i> 0.034; aOR 3.59, 95% CI 1.10–11.74), community-acquired bacteraemia (<i>P</i> 0.005; aOR 4.74, 95% CI 1.61–14.01) and age < 70 years (<i>P</i> 0.007; aOR 9.39, 95% CI 1.84–47.85). Conclusions: PJI was common among patients with documented <i>S. aureus</i> bacteraemia. PJI was associated with characteristics of the prosthesis, such as prior arthroplasty revisions and knee prosthesis.