Histone modifications play a crucial role in eukaryotic gene regulation. The Spt-Ada-Gcn5-acetyltransferase (SAGA) complex controls histone acetylation, with Gcn5 (GcnE) acting as the acetyltransferase. In the Aspergillus species, GcnE has been shown to regulate asexual development and secondary metabolism. Apart from this, GcnE is required for pathogenicity in plant fungal pathogen A. flavus; however, the role of GcnE in the pathogenicity of human pathogenic fungus A. fumigatus is unknown. In this study, we uncovered the key roles of GcnE in A. fumigatus conidiation, stress responses, and biofilm formation. We observed that deletion of gcnE resulted in aberrant conidiation in which conidiophores displayed abnormal phialide formation. In addition, the ΔgcnE mutant grew slightly faster under limited nitrogen sources (1 mM of ammonium or nitrate) compared to the wild type. The ΔgcnE mutant exhibited increased susceptibility to cell wall-perturbing agents, H2O2 and menadione but enhanced tolerance to LiCl. Furthermore, we showed that GcnE is involved in biofilm formation, and overexpression of adherence-related genes such as somA or uge3 partially rescued biofilm formation defects in the ΔgcnE mutant background. Interestingly, GcnE was not required for virulence in a neutropenic murine model of invasive aspergillosis. These results suggest that GcnE is critical for conidiation and biofilm formation but not virulence in A. fumigatus.