Background There are limited data which show how Emergency Department (ED)-specific knowledge and skills are acquired throughout the internal medicine fellowship, especially during 24-hour shifts. The aim of the study was to assess the differences in medical practice between fellows among different fellowship-years in ED settings. Methods We conducted a cross-sectional, retrospective study at a large university hospital using data on every ED examination done during 2016. All data were taken from the hospital information system. We compared 1st-year fellows with all older fellows, as well as 5th-year fellows with all younger fellows. Results In 2016, 55 fellows had ≥ 15 24-hour shifts with 3 attending fellows during one shift. A total of 19’916 patients were examined by attending fellows in the ED. When compared to 2nd-year fellows, 1st-year fellows examined more patients brought to ED by out-of-hospital emergency medical team and had significantly higher share of examined patients per 24-hour shift with lower length of stay. When compared to 5th-year fellows, 1st-year fellows examined older patients, but had lower share of examined patients during one 24-hour shift and participated in fewer CPR cases. When compared to younger fellows, 5th-year fellows participated in more CPR cases and had higher proportion of patients admitted to hospital. Conclusion To our knowledge, this is the first report on the ED medical practice differences among fellows of different fellowship-year. When compared to other fellows, 1st-year fellows participated less in CPR cases, but were faster in providing medical care in ED. 5th-year fellows had the highest proportion of patients admitted to hospital and more CPR cases.