Flutolanil is a broad-spectrum amide fungicide that is widely used to prevent fungal pathogens in agriculture. However, its usage may have a potential environmental impact on organisms. So far, few literatures have investigated the chronic toxicity of flutolanil at concentrations relevant to environmental conditions in the nontarget aquatic organisms. This study was aimed at evaluating whether the long-term exposure of flutolanil affects oxidative stress, immune response, and apoptosis in the liver of zebrafish ( Danio rerio). The results showed that the activity of catalase (CAT) was significantly decreased in the liver in all flutolanil-treated groups. Interestingly, the malondialdehyde (MDA) contents were remarkably increased following the flutolanil exposure. Deoxyribonucleic acid (DNA) damage was increased with a concentration-dependent manner. The transcription level of genes involved in apoptosis and the immune system were significantly altered following flutolanil chronic exposure in zebrafish liver. Furthermore, the caspase-3 enzyme activity was significantly increased. Taken together, this study demonstrated that the resulting effects on oxidative stress, immune toxicity, and apoptosis may be responsible for the pathological alterations in zebrafish liver after flutolanil exposure at concentrations relevant to environmental conditions, advancing the knowledge of pesticide environmental risk assessment.