<p>Ubiquitination is a key enzymatic process where ubiquitin molecules covalently attach to substrate proteins, regulating their degradation, trafficking, and signaling. This process ensures cellular homeostasis by controlling protein quality and abundance, and it plays a vital role in immunity, DNA repair, and the cell cycle. Further, ubiquitination involves a sophisticated network of enzymes, domains, and receptors, providing pathway flexibility. However, dysregulation of ubiquitination due to aberrant enzyme function is implicated in various disorders, including cancer, diabetes, stroke, and neurodegenerative diseases (NDDs). Additionally, the ubiquitin–proteasome system (UPS) not only mediates protein degradation but also influences inflammation and subcellular localization. This review explores the pivotal role of ubiquitination and deubiquitination enzymes in the onset and progression of NDDs. It highlights their involvement in protein aggregation, mitochondrial impairment, neuroinflammation, and altered synaptic function. Special focus is placed on mutations in E3 ligases (e.g., E3 ubiquitin ligase encoded by PARK2 (Parkin), C-terminus of Hsp70-interacting protein (CHIP)) and deubiquitinases (e.g., USP14, ubiquitin C-terminal hydrolases (UCHL1)), which disrupt proteostasis and lead to the accumulation of neurotoxic proteins, such as Aβ, tau, α-synuclein, and mHtt. Moreover, post-translational modifications (PTMs), including phosphorylation, acetylation, and oxidative stress, further modulate UPS activity and disease progression. Lastly, the review also evaluates emerging therapeutic strategies aimed at restoring proteostasis, including proteasome-targeting small molecules (e.g., bortezomib, IU1-47), natural compounds (e.g., curcumin, resveratrol), RNA-based therapies (e.g., miR-101, circHIPK3), and dietary approaches (e.g., Mediterranean and ketogenic diets), offering a foundation for future neurodegenerative disease treatment.</p>