The aim of this study is to examine the incidence trend of sepsis over 11 years and compared mortality outcomes among Taiwanese patients with sepsis admitted from emergency department (ED) and non-ED routes. We used a nationwide health insurance database from Taiwan, which comprise of 23 million beneficiaries. Patients with sepsis were identified by ICD-9 CM codes for infection and organ dysfunction from 2001 to 2012. We performed propensity score matching and compared mortality rates between ED-admitted and non ED-admitted patients.During the 11-year study period, we identified 1,256,684 patients with sepsis. 493,397 (29.3%) were admitted through the ED, and 763,287 (70.7%) were admitted directly to the floor. For patients with sepsis, mortality in ED-admitted patients decreased from 27.2% in 2002 to 21.1% in 2012 while that in non-ED admitted patients decreased from 35.3% in 2002 to 30.7% in 2012. Although patients with sepsis admitted through the ED had a higher incidence of organ dysfunction than patients who were directly admitted, they had more favorable outcomes in mortality, length of intensive care unit stay, and hospital stay. After propensity score matching, ED-admitted patients had a 7% lower risk of 90-day mortality (HR, 0.93, 95% CI, 0.89-0.97) compared with directly admitted patients. During the study period, mortality declined faster among ED admitted sepsis patients than directly admitted sepsis patients. Results of this study should be interpreted in light of limitations. Like other administrative database studies, treatment details are not available. Further clinical studies evaluating the treatment and outcome difference between ED and non-ED admitted sepsis patients are warranted.