Synaptopathies include a heterogeneous group of severely debilitating neurological diseases characterized by structural and functional deficits of neuronal synapses. Common synaptopathies include epilepsy, schizophrenia, prion diseases, autism spectrum disorders, various autoimmune diseases and cochlear synaptopathies. Their pathogenesis is caused by both genetic and environmental factors. However, the relationship between the cause and clinical manifestations of each particular synaptopathy, and their therapy, remain poorly understood. Here, we discuss animal models of synaptopathies, with a specific emphasis on zebrafish (Danio rerio), as well as outline several lines of future research in this field. Overall, zebrafish emerge as a promising organism to mimic a wide range of synaptopahies, paralleling and complementing their existing models in rodents.