A proteomic analysis of synaptic compartments obtained from septal-projecting hippocampal neurons revealed the formation of dystrophic neurites and synaptic loss at axon terminals as a result of the accumulation of numerous vesicles. Subsequent analysis also showed that toxic amyloid-β oligomers in the vicinity of dystrophic axons affected primary cilia, vesicle endocytosis, and neuronal exocytosis. The proteomic analysis of extracellular vesicles in presynaptic terminals confirmed that abnormal vesicle-mediated transport and exocytosis led to the accumulation of amyloid-β with extracellular vesicles at axon terminals. Further investigation showed that knockdown of the intraflagellar transport homolog 88 gene, which is essential for primary ciliogenesis in hippocampal neurons, led to an increase in amyloid-β uptake, leading to their accumulation with other synaptic vesicles at axon terminals.