Adverse maternal diets high in saturated fats are associated with impaired neurodevelopment and epigenetic modifications in offspring. Maternal milk, the primary source of early life nutrition in mammals, contains lactation-specific microRNAs (miRNAs). Lactation-specific miRNAs have been found in various offspring tissues in early life, including the brain. We examined the effects of maternal high saturated fat diet (mHFD) on lactation-specific miRNAs that inhibit DNA methyltransferases (DNMTs), enzymes that catalyze DNA methylation modifications, in the amygdala of female offspring during early life and adulthood. Offspring exposed to mHFD showed reduced miR-148/152 and miR-21 transcripts in stomach milk and amygdala in the first week of life. This was associated with increased DNMT1 expression, DNMT activity, and global DNA methylation in the amygdala. In addition, persistent DNA methylation modifications from early life to adulthood were observed in pathways involved in neurodevelopment as well as genes regulating the DNMT machinery and protein function in mHFD offspring. The findings indicate a novel link between exogenous, lactation-specific miRNAs and developmental programming of the neural DNA methylome in offspring.