Genetic risk variants in YWHAZ, encoding 14-3-ζ, have been found to contribute to psychiatric disorders such as autism spectrum disorder and schizophrenia, and have been related to an impaired neurodevelopment in humans and mice. Here, we have used a zebrafish model to further understand the mechanisms by which YWHAZ contribute to neurodevelopmental disorders. We first observed pan-neuronal expression of ywhaz during developmental stages, suggesting an important role of this gene in neural development. During adulthood ywhaz expression was restricted to Purkinje cells in the cerebellum, a region that shows alterations in autistic patients. We then established a novel stable ywhaz knockout (KO) zebrafish line using CRISPR/Cas9 genome engineering. We performed whole-brain calcium imaging in wild-type (WT) and ywhaz KO larvae and found altered neural activity and functional connectivity in the hindbrain. Interestingly, adult ywhaz KO fish also display decreased levels of dopamine and serotonin in the hindbrain and freeze when exposed to novel stimuli, a phenotype that can be reversed with fluoxetine and quinpirole, drugs that target serotonin and dopamine neurotransmission. Together, these findings suggest an important role for ywhaz in establishing neuronal connectivity during developmental stages. ywhaz deficiency leads to impaired dopamine and serotonin neurotransmission that may underlie the altered behaviour observed during adulthood.