Background: The seasonal influenza epidemic is an important public health issue worldwide. Early predictive identification of patients with potentially worse outcome is important in the emergency department (ED). Similarly as with bacterial infection, influenza can cause sepsis. This study was conducted to investigate the effectiveness of the Systemic Inflammatory Response Syndrome (SIRS) criteria and the quick Sequential Organ Failure Assessment (qSOFA) score as prognostic predictors for ED patients with influenza. Methods: This single-center, retrospective cohort study investigated data that was retrieved from a hospital-based research database. Adult ED patients (age ≥ 18 at admission) with laboratory-proven influenza from 2010 to 2016 were included for data analysis. The initial SIRS and qSOFA scores were both collected. The primary outcome was the utility of each score in the prediction of in-hospital mortality. Results: For the study period, 3561 patients met the study inclusion criteria. The overall in-hospital mortality was 2.7% (95 patients). When the qSOFA scores were 0, 1, 2, and 3, the percentages of in-hospital mortality were 0.6, 7.2, 15.9, and 25%, respectively. Accordingly, the odds ratios (ORs) were 7.72, 11.92, and 22.46, respectively. The sensitivity and specificity was 24 and 96.2%, respectively, when the qSOFA score was ≥2. However, the SIRS criteria showed no significant associations with the primary outcome. The area under the receiver operating characteristic curve (AUC) was 0.864, which is significantly higher than that with SIRS, where the AUC was 0.786 (P < 0.01). Conclusions: The qSOFA score potentially is a useful prognostic predictor for influenza and could be applied in the ED as a risk stratification tool. However, qSOFA may not be a good screening tool for triage because of its poor sensitivity. The SIRS criteria showed poor predictive performance in influenza for mortality as an outcome. Further research is needed to determine the role of these predictive tools in influenza and in other viral infections.