Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. The small heat shock protein HSPB1 is a ubiquitously expressed molecular chaperone and its S135F mutation has been linked to both axonal CMT and distal hereditary motor neuropathy. We previously revealed that the pathogenic interaction between S135F mutant and α-tubulin critically impairs autophagic clearance, resulting in proteostatic collapse and reduced neural stress adaptability. However, the therapeutic potential of targeting S135F/α-tubulin/autophagy axis in alleviating neuropathy remains unknown. In this study an integrative approach combining computational, biophysical and biochemical techniques was utilized to decipher the pattern of S135F/α-tubulin interaction and identify the potent disruptors to establish its therapeutic druggability. First, we revealed the β4/β8 groove in HSPB1 serving as the primary binding site for α-tubulin interaction. Then, through a structure-based drug repurposing strategy we identified fenebrutinib, a Bruton’s tyrosine kinase inhibitor, as a potent disruptor of the S135F/α-tubulin interaction through directly binding to β4/β8 groove. In both NSC-34 motor neuron and HEK293T cells, fenebrutinib ameliorated S135F-driven pathogenicity by reducing its binding to α-tubulin and consequently restoring autophagic flux. This led to enhanced clearance of misfolded proteins and improved neuronal resilience under stress conditions. Overall, our findings suggest that targeting the S135F/α-tubulin/autophagy axis holds significant promise as a therapeutic strategy for the preclinical intervention of CMT neuropathy, highlighting the importance of neuroprotection in early management of neurodegenerative disorders.