The aberrant formation and accumulation of the misfolded polyglutamine （polyQ） containing proteins in the nuclei are considered to be the major hallmark and cause of many neurodegenerative diseases, including Spinocerebellar ataxias （SCAs）, Huntington Disease （HD）, Spinal and Bulbar Muscular Atrophy （SBMA）, and Dentatorubro pallidoluysian atrophy （DRPLA）. It is, therefore, believed that intervening biosynthesis, resolution, and clearance of the misfolded proteins, may represent potential therapeutic approaches. Previous studies have found that the BFRF1 protein of the Epstein-Barr virus （EBV） promotes the translocation and clearance of nuclear mutant Huntingtin （Htt） inclusions in neuroblastoma cells. To investigate whether BFRF1 exhibits a similar effect in animals, BFRF1 was overexpressed in a Drosophila model of SCA3. We found that expression of BFRF1 did not cause damage to the development of Drosophila compound eyes. The retinal degeneration induced by polyQ-expanded Ataxin 3 （Atxn3） proteins was alleviated in flies overexpressing BFRF1. Overexpression of BFRF1 also reduced both soluble and insoluble Atxn3 proteins in flies. Although no improvement in lifespan was observed, overexpression of BFRF1 enhanced motor function in SCA3 flies. These results suggest that BFRF1 could suppress the toxicity mutant Atxn3 in flies. It was observed that BFRF1-containing vesicles engulf the protein aggregates and selectively fuse with autophagosomes, suggesting that the beneficial effects of BFRF1 in SCA3 flies could be mediated through autophagy.