Two representative pharmaceutical activated compounds, Carbamazepine and Naproxen, were removed (removal efficiency of 52.7 and 58.1%, respectively) in six days in a reaction system with the white-rot fungus Phanerochaete chrysosporium immobilized on sawdust. Naproxen's removal was considered mainly due to the biological/fungal removal whereas Carbamazepine's removal relied largely on the sawdust adsorption. The removal of two target compounds was not found directly related to the activities of two extracellular enzymes lignin peroxidase and manganese peroxidase, but the synthesis of two enzymes was inhibited by the addition of two pharmaceutical compounds at the initial period. The application of sawdust carriers was found conducive to the synthesis of extracellular enzymes even though without a significant improvement in the biomass production.