Rare diseases are characterized by a low prevalence, which often means that patients with such diseases are undiagnosed and do not have effective treatment options. Neurodevelopmental and neurological disorders make up around 40% of rare diseases and in the past decade, there has been a surge in the identification of genes linked to these conditions. This has created the need for model organisms to reveal mechanisms and to assess therapeutic methods. Different model animals have been employed, like Caenorhabditis elegans, Drosophila, zebrafish, and mice, to investigate the rare neurological diseases and to identify the causative genes. While the zebrafish has become a popular animal model in the last decade, mainly for studying brain development, understanding neural circuits, and conducting chemical screens, the mouse has been a very well-known model for decades. This review explores the strengths and limitations of using zebrafish as a vertebrate animal model for rare neurological disorders, emphasizing the features that make this animal model promising for the research on these disorders.