Significance Misfolding and accumulation of the protein α-synuclein (αS) inside nerve cells characterize Parkinson’s disease (PD) and related brain diseases, for which no disease-modifying therapies exist. Robust cell models are needed that recapitulate abnormal αS folding/accumulation in real time, especially for compound screening. We took advantage of the engineered αS “3K” (E35K+E46K+E61K) mutation, which amplifies the familial PD-causing E46K and readily forms round inclusions. We rescued the inclusions with known αS modulators and then screened a ∼2,000-compound library. We identified the potential therapeutic target stearoyl-CoA desaturase; its inhibition cleared αS inclusions, in accord with the effects of conditioning in saturated fatty acids. We propose a model for how fatty acids serve as key modulators of cellular αS homeostasis.