A high body temperature, i.e. fever, is a crucial vital sign, and suggests the patient’s infection or inflammation. COVID-19 has changed the lifestyle, and led to the changes in medical use behavior of febrile patients. We investigated the change in etiologies of fever in the emergency department (ED) before and after COVID-19. The medical records of patients with fever who visited the ED of a university hospital before and after the outbreak of COVID-19 in Daegu metropolitan city, South Korea. The cause of fever and its classification were carefully decided and established by agreement through a discussion among board-certified clinicians in emergency medicine, neurology, general surgery, and internal medicine. The etiology of fever and its prevalence in ED were compared between before and after COVID-19. A total of 3,041 patients with fever (> 37.7°C) in the ED were investigated, with 1,400 men (46.0%). Their mean age was 55.88 ± 20.59, and the average number of patients with fever in ED was 8.16 ± 3.94 per a day. The most common etiology before COVID-19 was respiratory system infection (n = 535, 30.5%), followed by gastrointestinal (n = 313, 17.8%) and urinary tract infection (n = 209, 11.9%). However, after COVID-19, gastrointestinal cause became the most common (n = 247, 27.3%), followed by respiratory system (n = 126, 13.9%) and urinary tract infection (n = 102, 11.3%). There has been paradigm-shifting in fever etiology in the emergency department. It is necessary to cope with the changed fever etiology in the COVID-19 era.