Maternal malnutrition, including obesity, can have long-term adverse effects on offspring health, potentially mediated by epigenetic mechanisms such as microRNAs (miRNAs). These miRNAs play a critical role in regulating gene expression and may contribute to the developmental programming of offspring outcomes. This systematic review aimed to explore the association between maternal obesity during pregnancy and miRNA alterations in offspring, focusing on evidence from animal models. A comprehensive search of the Embase, PubMed, and Scopus databases identified 811 articles, 15 of which met the inclusion criteria. Our analysis revealed significant variability in the miRNAs and target tissues studied. Across the reviewed studies, 35 miRNAs were identified as differentially expressed in offspring exposed to maternal high-fat diet during pregnancy. These alterations were predominantly observed in the brain, liver, cardiac tissue, and adipose tissue, affecting processes related to insulin signaling, development and growth, immune response, and lipid metabolism. The observed miRNA alterations support the hypothesis that a maternal high-fat diet may induce a programmed epigenetic signature in offspring.