Palmitoylation is a reversible lipid modification, regulating protein localization and signaling in neurons. Growth-associated protein 43 (GAP43) requires palmitoylation for axonal development and synaptic plasticity; however, its depalmitoylase and regulation in neural circuits remain unknown. We investigated whether palmitoyl-protein thioesterase 1 (PPT1) is the principal depalmitoylase for GAP43 and examined how disrupted PPT1-GAP43 signaling affects neuronal morphology and circuit function. Using biochemical assays, structural modeling, CRISPR-Cas9–generated GAP43 point mutation mice (GAP43-PM), PPT1-knockout mice (PPT1-KO), electrophysiology, and behavior, we demonstrated that PPT1 interacts with GAP43 at Cys 3 and Cys 4 to mediate its depalmitoylation, disruption of this interaction causes GAP43 hyperpalmitoylation that drove excessive dendritic arborization and aberrant growth cone expansion, enhanced glutamatergic transmission, and hippocampal network hyperexcitability, resulting in cognitive deficits without lysosomal storage pathology. Exogenous PPT1 reduced these morphological/synaptic abnormalities. Our findings establish the PPT1-GAP43 depalmitoylation pathway as essential for neuronal circuit homeostasis; its dysfunction contributes to neurodevelopmental disorders, identifying a potential therapeutic target for palmitoylation-related neurodevelopmental disorders.