We performed a comparative study to determine the proteome of extracellular vesicles (EVs) from the cereal pathogen Fusarium graminearum (Fgr), recovered from in vitro cultures. Label-free quantitative proteomics was used to find significant enrichment of proteins between EV samples, the secretome (secreted-soluble proteins) and the cell lysate. Our results show that some proteins were exclusive to EVs and were upregulated compared to the secretome or cell lysate.