Copper nanoparticles (Cu NPs) are a new pollutant in aquaculture, representing a hazard to aquatic organisms. We investigated the effects of Cu NPs exposure on oxidative stress, apoptosis and immune response in an economically important model species, Takifugu fasciatus. The juvenile fish were exposed to control, 20 or 100 μg Cu NPs/L for 30 days. The growth of T. fasciatus was inhibited after Cu NPs exposure. Copper accumulation in liver increased with increasing Cu NPs dose. Oxidative stress indicators [malondialdehyde (MDA), total superoxide dismutase (T-SOD), catalase (CAT) and glutathione (GSH)], apoptosis index and activities of caspases (caspase-3, caspase-9) were all increased with the increase of Cu NPs concentration in liver. With an increase in Cu NPs dose, the activities of succinate dehydrogenase (SDH) and Na-K-ATPase as well as cytochrome c (Cyt-c) concentration in mitochondria decreased, accompanied by increased Cyt-c concentration in cytosol. Apoptosis-related gene expressions of p53, caspase-3, caspase-9 and Bax were increased with the increase of Cu NPs dose. However, the opposite result was found in Bcl2 expression. The physiological indicators of immune response [heat shock protein 70 (HSP70), heat shock protein 90 (HSP90), immunoglobulin M (IgM) and lysozyme (LZM)] as well as the mRNA levels of HSP70, HSP90, IgM and C-LZM were all increased after Cu NPs exposure. Our results will be helpful in understanding the mechanism of Cu NPs toxicity in T. fasciatus.