Aim A potentially safe disposal method for copper-containing waste wood is bioremediation using brown-rot fungi. However, the mechanisms regulating brown-rot fungi copper tolerance are poorly understood. The objective of this study was to better understand the molecular and physiological changes in Polyporales sp. KUC9061 in response to Cu(II) using GeneFishing technology. Methods and Results The presence of Cu(II) in the malt extract agar (MEA) media decreased the brown-rot fungi's growth rate in a concentration-dependent manner, but the fungal biomass was significantly increased in part for the biosorption of Cu(II). Increased expression of the genes encoding for the GIS2 DNA-binding protein and the 40S ribosomal protein S3A appears to be involved in this process. Oxalic acid is not used as a defence mechanism against high copper exposure, and ATP citrate lyase is not directly involved in oxalic acid production in this fungus. Several Cu(II)-sensitive proteins showed stable gene expression, suggesting that mechanisms that do not rely on these genes are responsible for the Cu(II) tolerance of the fungus. Conclusions Polyporales sp. KUC9061 does not use oxalic acid to chelate excess Cu(II) and potentially has other mechanisms, including the increased production of mycelia, to regulate Cu(II) biosorption. Significance and Impact of the Study This study is the first effort to examine Cu(II)-induced differential gene expression and the related physiological changes in the brown-rot fungus, a potential degrader of copper-containing waste wood. The results of this study will help with using this fungus to safely dispose of waste wood safe.