A rotating suspension cartridge reactor immobilized with white-rot fungus Phanerochaete chrysosporium was employed to treat synthetic wastewater containing 1000 μg l^-1of the recalcitrant pharmaceutically active compound carbamazepine. The reactor was continuously operated for 160 days under non-sterile conditions. After one month of fungal adaptation, the removal efficiency for carbamazepine exceeded 90% through such strategies as the immobilization of P. chrysosporium on the polyurethane foam cubes (1.0 × 1.0 × 1.0 cm³), the pattern of liquid/air flow inside the cartridge created through the application of intermittent operational mode, and the gradual cut of external carbon source loading in the influent. Both nutrients and oxygen were effectively transferred to fungi, which contributed to the excellent bioreactor treatment performance for the long-term continuous operation. The bacterial contamination occurring in the bioreactor was effectively suppressed, providing a feasible alternative to treat recalcitrant compounds under non-sterile conditions.