Aerobic biodegradation combined with pyrite-Fenton process was used for the treatment of wastewater containing different chlorophenols (4-CP, 2,3-DCP, 2,4-DCP, 2,4,6-TCP). Fenton degradation using pyrite as the low cost iron catalyst was used as a pre-treatment step to lower the toxicity of CPs prior to aerobic biodegradation. Synthetic wastewater spiked directly with either 100 mg/L CPs or pyrite-Fenton pre-treated CPs was fed to the batch bioreactors inoculated with unacclimated or acclimated activated sludge using glucose as the C-source. The results show that the CP biodegradation under aerobic conditions was highly dependent on the type of CP treated. Except for 2,4-DCP, all other CPs investigated caused severe sludge toxicity, and thus significantly hindered glucose degradation by unacclimated sludge. The CP toxicity decreased in the order of: 2,4,6-TCP > 2,3-DCP > 4-CP > 2,4-DCP. The toxic effect was explained through an interaction of CPs with the lipid fraction of cell membrane. While the pyrite-Fenton pre-treatment improved the COD removal efficiency using unacclimated sludge, the sCOD removal efficiency was still less than the control reactor operated with no CP addition. With sludge acclimation, however, the sCOD removal efficiencies increased, and approached 74% for 2,4-DCP, 61% for 4-CP, 56% for 2,4,6-TCP and 46% for 2,3-DCP, suggesting an enhanced biomass tolerance to CP toxicity. On the other hand, the sludge acclimation combined with pyrite Fenton pre-treatment provided the best bioreactor performance for all CPs with the sCOD removal efficiencies reaching 81% for 2,4,6-TCP, 78% for 2,4-DCP, 73% for 4-CP and 62% for 2,3-DCP. This suggests that the dechlorination of CPs with Fenton process, in conjunction with sludge acclimation, not only reduced the sludge toxicity, but also enhanced the bioavailability of CP-containing wastewater for microorganisms, especially for highly chlorinated toxic CPs such as 2,4,6-TCP. Overall, the findings highlight the need for sludge acclimation for effective treatment of chlorophenol-containing wastewater by a combined pyrite-Fenton and aerobic biodegradation system.