Lysosome axonal transport is important for the clearance of cargoes sequestered by the endocytic and autophagic pathways. Building on observations that mutations in the JIP3 (MAPK8IP3) gene result in lysosome-filled axonal swellings, we analyzed the impact of JIP3 depletion on the cytoskeleton of human neurons. Dynamic focal lysosome accumulations were accompanied by disruption of the axonal periodic scaffold (spectrin, F-actin and myosin II) throughout each affected axon. Additionally, axonal microtubule organization was locally disrupted at each lysosome-filled swelling.This axonal microtubule disorganization in JIP3 KO neurons was accompanied by increased tau abundance and phosphorylation. These results indicate that transport of axonal lysosomes is integrated into a much larger network that is required for the maintenance of the axonal cytoskeleton. These findings have potential relevance to human neurological disease arising from JIP3 mutations as well as for neurodegenerative tauopathies such as Alzheimer's disease.