The ECDC Fellowship Programme is a two-year training program consisting of two distinct pathways: field epidemiology (EPIET) and public health microbiology (EUPHEM). EPIET was created in 1995 with the purpose of creating a network of highly trained field epidemiologists in the European Union, thereby strengthening the public health epidemiology workforce within European Union (EU) and European Economic Area (EEA) member states. EPIET was integrated with ECDC in 2006. EUPHEM was initiated by ECDC in 2008. In 2016, EPIET and EUPHEM became the ECDC Fellowship Program, consolidating alignment of administrative processes and core curricular aspects.

Each path in the ECDC fellowship program comprises two tracks: the EU track and the member state (MS) track. In the EU track, citizens of an EU or European Economic Area (EEA) member state apply individually. Fellows are selected by the ECDC, and for the duration of their training, they are assigned to a member state that differs from that of their own nationality. For graduates of the EU track, there is the opportunity for mobility, thereby strengthening field epidemiology and microbiology professionals throughout the EU. In the MS track, member states apply to ECDC for a fellowship post to train professionals currently in their workforce. Applicants are selected by their own member state and remain in their country of residence or citizenship for the duration of their training. The aim is to retain qualified graduates in their country. Both tracks follow the same curriculum but have different selection procedures. The program is competency-based and fellows are placed at recognized training sites across the EU and EEA member states.