Rapid organism detection of Staphylococcus aureus bacteremia and communication to clinicians expedites antibiotic optimization. We evaluated clinical and economic outcomes of a rapid polymerase chain reaction methicillin‐resistant S. aureus/S. aureus blood culture test (rPCR). This single‐center study compared inpatients with S. aureus bacteremia admitted from 1 September 2008 through 31 December 2008 (pre‐rPCR) and those admitted from 10 March 2009 through 30 June 2009 (post‐rPCR). An infectious diseases pharmacist was contacted with results of the rPCR; effective antibiotics and an infectious diseases consult were recommended. Multivariable regression assessed clinical and economic outcomes of the 156 patients. Mean time to switch from empiric vancomycin to cefazolin or nafcillin in patients with methicillin‐susceptible S. aureus bacteremia was 1.7 days shorter post‐rPCR (P = .002). In the post‐rPCR methicillin‐susceptible and methicillin‐resistant S. aureus groups, the mean length of stay was 6.2 days shorter (P = .07) and the mean hospital costs were $21,387 less (P = .02). rPCR allows rapid differentiation of S. aureus bacteremia, enabling timely, effective therapy and is associated with decreased length of stay and health care costs.