Misfolded proteins that evade chaperone-mediated refolding and proteasome-dependent degradation can form aggregates in cells. These protein aggregates are cytotoxic and are linked to several neurodegenerative diseases, including Alzheimer’s and Huntington’s diseases. However, the aggregates can further form a cytoprotective structure termed an aggresome (inclusion body), and studies in higher eukaryotes indicate that K63-linked ubiquitination promotes aggresome formation for some substrates. Polyglutamine (polyQ) expansion within Huntingtin protein contributes to the development of Huntington’s disease and expression of mutated Huntingtin with 103 polyQ (Htt103QP) leads to aggresome formation in both mammalian and yeast cells. Using yeast as a model organism, we demonstrate that Htt103QP is degraded primarily through the proteasome prior to aggresome formation, while vacuole (lysosome)-dependent autophagy pathway is responsible for Htt103QP clearance once an aggresome is formed. We further show that K63-linked ubiquitination promotes aggresome formation of Htt103QP, as abolishment of K63 ubiquitination in yeast cells compromises aggresome formation. The observation that mutation of the three lysine (K) residues in the N-terminus of Htt103QP resulted in aggresome formation defect indicates that ubiquitination of Htt103QP itself contributes to aggresome formation. In addition, we found that the E3 ubiquitin ligase Rsp5 (Nedd4) promotes K63-linked ubiquitination of Htt103QP and is required for aggresome formation. Therefore, we can use yeast as a model organism to study the clearance process for misfolded proteins linked to neurodegenerative diseases.