Endogenous oxidative damage to brain mitochondrial DNA and mitochondrial dysfunction are contributing factors in aging and in the pathogenesis of a number of neurodegenerative diseases. In this study, we characterized the regulation of base‐excision‐repair (BER) activity, the predominant repair mechanism for oxidative DNA lesions, in brain mitochondria as the function of age. Mitochondrial protein extracts were prepared from rat cerebral cortices at the ages of embryonic day 17 (E17) or postnatal 1‐, 2‐, and 3‐weeks, or 5‐ and 30‐months. The total BER activity and the activity of essential BER enzymes were examined in mitochondria using in vitro DNA repair assay employing specific repair substrates. Mitochondrial BER activity showed marked age‐dependent declines in the brain. The levels of overall BER activity were highest at E17, gradually decreased thereafter, and reached to the lowest at the age of 30‐month (∼80% reduction). The decline of overall BER activity with age was attributed to the decreased expression of repair enzymes such as 8‐OHdG glycosylase and DNA polymerase‐γ and, consequently, the reduced activity at the steps of lesion‐base incision, DNA repair synthesis and DNA ligation in the BER pathway. These results strongly suggest that the decline in BER activity may be an important mechanism contributing to the age‐dependent accumulation of oxidative DNA lesions in brain mitochondria.