This study assessed the impacts of atrazine (ATR), chlorpyrifos (CPF), and a combined ATR/CPF exposure on the brain of common carp (Cyprinus carpio L.). The carp were sampled after a 40-days exposure to CPF and ATR, individually or in combination, followed by a 40-days recovery period to measure autophagy and antioxidant activity. The results indicate that the anti-superoxide anion and anti-hydroxy radical activities decreased upon exposure to ATR, CPF, and the ATR/CPF combination but increased after a subsequent 40-days recovery period. Quantitative real-time PCR and Western blot analyses revealed that the mRNA and protein levels of LC3B and dynein in common carp decreased significantly after exposure to ATR and CPF alone or in combination. Moreover, the mRNA and protein levels of beclin1 gene decreased significantly only in the 116 and 11.3 μg/L treatment groups. However, the mRNA and protein levels of all tested genes increased significantly after a 40-days recovery. Transmission electron microscope demonstrated the occurrence of autolysosomes in the recovery groups but not in the exposure groups. These results suggest that exposure to ATR, CPF, or their combination promotes oxidative stress and autophagic responses in the brain of common carp.