Protein palmitoylation, a prevalent and dynamic form of S-acylation modification, plays a critical role in maintaining the functionality of the nervous system. This reversible process involves the attachment of palmitic acid to cysteine residues in proteins, anchoring them to cellular membranes and regulating their spatial distribution. The functioning of palmitoylation is crucial for normal neuronal activities, influencing key processes such as signal transduction, synaptic function, and protein trafficking. Recent research has increasingly underscored the significance of specific zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases in neuronal development and synaptic plasticity. These enzymes, which catalyze the palmitoylation of proteins, have emerged as pivotal regulators of brain function. Dysregulation of palmitoylation by these enzymes is now recognized as a potential contributor to the pathogenesis of various neurodegenerative diseases. This review provides an in-depth analysis of the expression patterns and functional diversity of ZDHHC enzymes across different brain regions and cell types. ZDHHC enzymes exhibit significant sequence variability and demonstrate region-specific and cell type-dependent expression. Such heterogeneity suggests that these enzymes may have specialized roles in different areas of the nervous system, making them crucial modulators of neuronal function and synaptic transmission. The review also explores the regulatory mechanisms of protein palmitoylation and their implications in neurodegenerative disease onset and progression. Altered palmitoylation can lead to the destabilization and subsequent aggregation of these proteins, exacerbating neurodegenerative processes. Abnormal palmitoylation of α-synuclein can either promote or inhibit its aggregation in Parkinson’s disease pathology. Proteins related to these key pathological factors, including amyloid precursor protein (APP) and beta-secretase 1 (BACE1), are also influenced by palmitoylation, contributing to the formation of amyloid plaques through the aggregation of Aβ. Additionally, ZDHHC13 and ZDHHC17, which are abundantly and widely expressed in the brain, play crucial roles in this process. For instance, reduced interaction between ZDHHC17 and huntingtin could significantly contribute to the pathogenesis of Huntington’s disease. Thus, modulating the palmitoylation status of these proteins presents a promising therapeutic strategy to prevent their toxic aggregation and mitigate neuronal damage. Actually, regulating palmitoylation has shown potential for therapeutic interventions in neurodegenerative diseases, with studies demonstrating that modulation of palmitoylation can restore neuronal function and improve disease symptoms. Regulating palmitoylation holds significant promise for therapeutic strategies in neurodegenerative diseases, as modulation of this process can restore neuronal function and ameliorate disease symptoms. However, progress is hindered by the lack of high-resolution structural data and comprehensive targeting maps for specific ZDHHC enzymes. Additionally, current detection methods for palmitoylation, which focus on labeling and analyzing palmitic acid and cysteine residues, are often complex and time-consuming, and may produce inconsistent palmitoyl-proteomic profiles. These methodological challenges underscore the need for more robust and efficient detection technologies. A deeper understanding of palmitoylation’s role in neurological diseases, coupled with the development of improved detection methods, is essential for advancing our knowledge of the molecular underpinnings of these conditions and for the creation of innovative therapeutic strategies aimed at combating neurodegenerative diseases.