Palmitoylation is a key post-translational modification mediated by a family of DHHC-containing palmitoyl acyl-transferases (PATs). Unlike other lipid modifications, palmitoylation is reversible and thus often regulates dynamic protein interactions. We find that the mouse hair loss mutant, depilated, (dep) is due to a single amino acid deletion in the PAT, Zdhhc21, resulting in protein mislocalization and loss of palmitoylation activity. We examined expression of Zdhhc21 protein in skin and find it restricted to specific hair lineages. Loss of Zdhhc21 function results in delayed hair shaft differentiation, at the site of expression of the gene, but also leads to hyperplasia of the interfollicular epidermis (IFE) and sebaceous glands, distant from the expression site. The specific delay in follicle differentiation is associated with attenuated anagen propagation and is reflected by decreased levels of Lef1, nuclear β-catenin, and Foxn1 in hair shaft progenitors. In the thickened basal compartment of mutant IFE, phospho-ERK and cell proliferation are increased, suggesting increased signaling through EGFR or integrin-related receptors, with a parallel reduction in expression of the key differentiation factor Gata3. We show that the Src-family kinase, Fyn, involved in keratinocyte differentiation, is a direct palmitoylation target of Zdhhc21 and is mislocalized in mutant follicles. This study is the first to demonstrate a key role for palmitoylation in regulating developmental signals in mammalian tissue homeostasis., Author Summary During embryonic development, growth and patterning are regulated at many levels. Signals that mediate transcriptional activity, where and when genes are expressed, are a primary level of regulation. However, developmental signals can be further fine-tuned by modulating protein stability, localization, and activity via post-translational modifications. One such modification is the reversible addition of the fatty acid palmitate to proteins. This modification mediates dynamic trafficking of target proteins to specific subdomains of the cell. A large family of enzymes carries out this palmitoylation process, where each family member has specificity towards particular targets. However, the functional significance of palmitoylation during mammalian development is unclear. We present evidence of a critical role for palmitoylation during mouse development using a mutation of a specific palmitoylating enzyme, whose loss of function leads to hair loss and skin defects in depilated (dep) mice. Despite its restricted expression in hair follicles, loss of function of this enzyme results in developmental defects in nearby structures. We show that palmitoylation plays an important regulatory role in hair growth and epidermal homeostasis.