Synaptopathies represent a heterogeneous group of severe, debilitating neurological diseases characterized by structural and functional synaptic deficits. 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, as well as their therapy, remain poorly understood. Here, we discuss animal models of synaptopathies with a special focus on zebrafish (Danio rerio) and outline several lines of future research in this field. Overall, the zebrafish emerges as a promising organism to mimic a wide range of synaptopahies, paralleling and complementing their existing models in rodents.