We developed a new method for monitoring the distribution of administrated fatty acids in the body by combination of a stable isotope-labeling technique and imaging mass spectrometry (IMS). The developed stable isotope-labeling technique is very simple and able to adapt to all the fatty acid species. In this study, we synthesized stable isotope-labeled arachidonic acid (AA) and docosahexaenoic acid (DHA), and they were simultaneously administrated to mice to examine their migrations and distributions in the brain. The administrated AA and DHA have two more molecular weights compared to the originals and apparently were distinguished from the originally accumulated AA and DHA in the brain using IMS. As a result, we reveal that the administered AA and DHA first accumulated in the hippocampus and cerebellar cortex in the brain. This technique does not use radio isotopes and would appear to elucidate the role of all kinds of fatty acid species in the body.