<p>Enamel maturation depends on the ability of ameloblasts to undergo repeated cycles of morphological remodeling, a process known as ameloblast modulation. These transitions require precise coordination between cytoskeletal reorganization and vesicular trafficking, yet the intracellular mechanisms that support this coordination remain unclear. Although mutations in the <i>Wdr72</i> gene cause enamel defects, the cellular role of WDR72 during enamel maturation has not been defined. Here, we investigated whether WDR72 functions within the microtubule-dependent vesicular trafficking machinery and whether disrupting this function alters vesicular-mediated microRNA (miRNA) export during ameloblast modulation. Using <i>Wdr72</i> functional knockout (fKO) mouse and cell models, we examined WDR72 function in relation to microtubules, CD63-positive (CD63⁺) multivesicular bodies (MVBs) that carry vesicles destined for extracellular vesicles (EVs) along microtubules, and miRNA export via EVs. We found that WDR72 associates with microtubules in ameloblast-lineage cells. Loss of WDR72 function disrupts this association without preventing MVB engagement with microtubules. Instead, <i>Wdr72</i>-fKO cells exhibit intracellular accumulation of CD63⁺ vesicles, indicating impaired MVB transit or vesicle export, accompanied by reduced vesicle-associated miRNA export. Integration of miRNA and mRNA expression profiles from <i>Wdr72</i>-deficient enamel organs revealed an inverse relationship between accumulated circulating miRNAs and reduced levels of their predicted target transcripts, which are enriched for cytoskeletal genes essential for maintaining ameloblast morphology and polarity. Together, these findings identify WDR72 as a microtubule-associated protein that links vesicular miRNA export to enamel maturation and show that disruption of this pathway impairs ameloblast modulation during enamel mineralization.</p>