Yearly seasonal influenza pandemic has been an important public health issue around the world. There had been 2 major outbreaks in Taiwan in 2009 and 2016. More than 100 severe complicated influenza cases were reported to the Center of Disease Control, Taiwan. Mortality rate was about 30% among these patients. Early prediction of patients with potentially worse outcome is important in the emergency department. Sepsis-3 was the latest definition of sepsis published in 2017. qSOFA score had been developed as the initial evaluation tool of sepsis. In this study, we aimed to investigate the effectiveness of qSOFA score as a prognosis predictor of patients with influenza in the emergency department. This is a single-centered, retrospective cohort study. All the data were retrieved from a hospital-based research database. Adult patients (age ≧ 18 at admission) with a positive influenza rapid screening test or a positive Influenza virus polymerase chain reaction (PCR) from 2010 to 2016 were enrolled for data analysis. qSOFA score and systemic inflammatory response syndrome (SIRS) in the emergency department were both collected. Patients’ data including basic characteristics, hospitalization status, and outcome were collected. The primary outcome is the performance of both scores in predicting in-hospital mortality. In the study period, 3,561 patient visits met the inclusion criteria. Mean patient’s age was 48.1 ± 19.5 with nearly equal sex distribution (48.2 % male). 1,527 patients (42.9%) were admitted to the hospital. 286 patients (8%) were admitted to the intensive care unit (ICU). The overall in-hospital mortality was 2.7%. with an overall in-hospital mortality rate of 2.7% (95 patients). When qSOFA score is 0, 1, 2, and 3, the percentage of hospital admission was 34.3%. 66.7%, 80.4%, and 75%, respectively. Accordingly, the in-hospital mortality was 0.6%, 7.2%, 15.9%, and 25%, respectively. The odds ratios of in-hospital mortality were 7.72 (4.35-13.70, 95% confidence interval), 11.92 (5.74-24.77), and 22.46 (4.33-116.61) when qSOFA score was 1, 2, and 3, respectively (all p value < 0.001). The odds ratios of ICU admission were 7.21 (5.35-9.73), 12.54 (8.04-19.56), and 38.7 (11.73-127.72) when qSOFA score was 1, 2, and 3, respectively (all p<0.001). The sensitivity and specificity of when aSOFA score ≧ 2 was 24% and 96.2%, respectively. Area under depicted ROC curve was 0.864, which is significantly higher compared to SIRS criteria, which was 0.786 (p < 0.01). Influenza infection was usually a self-limited disease with low in-hospital mortality. Disease progression of severe complicated influenza might develop in a very short time interval. qSOFA score at presentation in the emergency department greater than 2 was a prognostic predictor for both ICU admission and in-hospital mortality but it should not be used to exclude further deterioration due to its poor sensitivity.