This study aimed to compare the alterations on expression patterns of exosomal microRNAs between invasive aspergillosis patients and healthy controls. A small experimental study was designed to measure the expression rate of 14 different exosomal microRNAs in different patient groups which might be linked to invasive fungal infections. Among them, 9 different microRNAs were significantly down-regulated in proven (P1) and probable (P2) cases in comparison to possible (P3) controls. Diagnostic performance of exosomal microRNA biomarkers were evaluated with different combinations of differentially expressed exosomal microRNAs. In summary, this experimental approach showed the differential expression of exosomal microRNAs which might be involved in invasive aspergillosis pathogenesis and can also serve as diagnostic biomarkers for early detection of IA and its treatment.