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The aim of the present study was to investigate the possible relationship between the levels of various fatty acids (FA) in the brain and learning indices in aged (22–23 months old) and young (2–3 months old) female Swiss Webster (SW) mice. The mice were classified as “good” or “poor” learners based on their performance in a spatial learning task: the Morris Water Maze. The levels of several FA including palmitic, stearic, oleic, linoleic, arachidonic (AA), and docosahexaenoic acid (DHA), were measured by gas chromatography in tissue samples from four different brain areas: hippocampus, frontal cortex, striatum and hypothalamus. The results of behavioral tests confirmed a decline in learning skills with age. However, a great individual variation was revealed in learning scores between aged subjects, indicating that biological aging does not always parallel chronological aging. The relative levels of particular fatty acids across the four examined brain structures were very similar. Interestingly, only in the hypothalamus was the DHA omega-3 acid level significantly higher in young mice compared to the old mice. For the remaining brain structures, no significant correlations were found between the DHA level and the animal's age and/or cognitive status. A significant correlation between learning performance and fatty acid levels in the brain was found only for AA in the young mice hippocampus, a structure known to be critical for spatial learning and memory. The AA level was significantly lower in young “good” learners compared to both young “poor” and old “good” learners with young “good” learners showing significantly better performance than the two other groups. These findings contribute to the current debate on the value of DHA supplementation as an effective protective treatment against senile dementia and the potential role of AA in memory deficits.