Background: We investigated the effect of antibiotic timing on outcomes based on changes in surrogate markers of organ failure, including platelet, serum bilirubin, serum creatinine levels, and the PaO2/FiO(2) (P/F) ratio. Methods: This was a single-center, retrospective observational study of critically ill septic patients who presented to the emergency department (ED). The study period extended from August 2008 to September 2016. The primary outcomes included changes in platelet, serum bilirubin, serum creatinine levels, and the P/F ratio (delta-platelet, delta-serum bilirubin, delta-serum creatinine, and delta-P/F ratio were calculated as values measured on Day 3; values measured at ED enrollment). A multivariable linear regression model was developed to assess variables related to outcomes (delta-platelet, delta-serum bilirubin, delta-serum creatinine, and delta-P/F ratio). Results: We analyzed 1784 patients who met the inclusion criteria. The overall 28-day mortality was 14% (n = 256/1784). On multivariable linear regression analysis, the hourly delay in antibiotic therapy was significantly associated with a decrease in delta-platelet count (coefficient, -1.741; standard error, 0.740; p = 0.019), and an increase in delta-serum bilirubin (coefficient, 0.054; standard error, 0.021; p = 0.009). In contrast, it was not associated with delta-creatinine (coefficient, 0.008; standard error, 0.010; p = 0.434) or the delta-P/F ratio (coefficient, -0.797; standard error, 1.858; p = 0.668). Conclusion: The hourly delay of antibiotic therapy was associated with decreased platelet count and increased serum bilirubin concentration in critically ill septic patients during the first three days of ED admission.