N-3 polyunsaturated fatty acids (n-3 PUFA) are known to have cardiovascular and neuroprotective properties in both humans and rodents. Here, we use manganese-enhanced magnetic resonance imaging (MEMRI) to compare the effects of these polyunsaturated fatty acids on the combined effects of neuronal activity and integrity of blood–brain barrier integrity with saturated fatty acids from buttermilk. C57BL/6 mice (4 weeks old) were fed isocaloric diets containing 3% fish oil (3% FO, n = 5), 12% fish oil (FO, n = 6), 3% buttermilk (3% BM, n = 6) or 12% buttermilk (12% BM, n = 6) for 6 months. Following metabolic cage analysis these mice were scanned using a standard MEMRI protocol at 28–32 weeks of age. Adult mice aged 28–32 weeks old (RM3, n = 5) and 15–16 weeks old (YRM3, n = 4) maintained on standard rodent chow were also studied to assess age-related changes in brain barrier systems and neuronal activity. Signal intensity (SI) in the anterior pituitary (AP), arcuate hypothalamic nucleus (ARC), ventromedial hypothalamic nucleus (VMH) and the paraventricular hypothalamic nucleus (PVN) was significantly reduced in young compared to older mice fed standard chow. Furthermore, fish oil supplementation led to a decrease in SI within the ARC and PVN, reaching significance in the VMH in age-matched controls. Interestingly, both fish oil and buttermilk supplementation resulted in a significant increase in SI within the AP, a structure outside the BBB. We conclude that MEMRI is able to detect the combined effects of the integrity of neuronal activity and blood–brain barrier permeability in the hypothalamus associated with dietary manipulation and aging.