Glia serve as double-edged swords to modulate neuropathology in Parkinson’s disease (PD), but how they react opposingly to be beneficial or detrimental under pathological conditions, like promoting or eliminating α-synuclein (α-syn) inclusions, remains elusive. Here we present evidence that dAuxilin (dAux), the Drosophila homolog of the PD risk factor Cyclin G-associated kinase (GAK), regulates the lysosomal degradation of α-syn in glia. Lack of glial Gak/dAux increases the lysosome number and size, regulates lysosomal acidification and hydrolase activity, and ultimately blocks the degradation of substrates including α-syn. Whereas α-syn accumulated prominently in lysosomes devoid of glial dAux, levels of injected α-syn preformed fibrils also further enhanced in the absence of microglial Gak. Mechanistically, dAux mediates phosphorylation at the serine 543 of Vha44, the V1C subunit of the vacuolar H + -ATPase (V-ATPase), regulates its assembly to control proper acidification of the lysosomal milieu. Expression of Vha44, but not the Vha44 variant lacking S543 phosphorylation, restores lysosome acidity, locomotor deficits, and DA neurodegeneration upon glial dAux depletion, linking this pathway to PD. Our findings identify a phosphorylation-dependent switch controlling the V-ATPase assembly for lysosomal α-syn degradation in glia. Targeting the clearance of glial α-syn inclusions via this lysosomal pathway could potentially be a therapeutical approach to ameliorate the disease progression in PD.