Mycoviruses are a specific group of viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, is recently shown to harbour at least three different types of mycoviruses. RNA silencing mechanisms exist in fungi against mycoviruses and it is also known that A. fumigatus encodes all the proteins involved in RNA silencing, including Dicer and Argonaute homologues. Therefore, it is anticipated that small interfering RNAs (siRNAs) are generated and silencing of viral dsRNAs occurs as seen with other mycoviruses. This study compares the gene expression levels in isogenic lines of virus-free and virus-infected A. fumigatus. Eight different genes that play a role in RNA silencing were selected and analysed by quantitative PCR in order to determine whether the expression levels of these genes correlate with virus infection. To further evaluate the potential existence of siRNAs, small RNA profiles of virus-free and virus-infected isolates were compared using next generation sequencing. Virus-derived siRNAs were detected in the presence of three A. fumigatus virus infections. Moreover first miRNA-like candidates in A. fumigatus were identified. Additionally, the effects of mycoviruses on the pathogenicity of A. fumigatus were assessed using larvae of the greater wax moth Galleria mellonella. A. fumigatus uncharacterised virus was found to cause mild hypervirulence in A. fumigatus. To our knowledge this is the first study reporting the small RNA profiles of A. fumigatus isolates and also the interaction between mycoviruses and virulence of A. fumigatus.