This study aimed to investigate the effect of European bilberry extract (EBE) on the accumulation of Nε-carboxymethyllysine (CML) and Nε-carboxyethyllysine (CEL) in rats exposed to a high advanced glycation end products (AGEs) diet. We found that EBE reduced high AGEs diet-induced accumulation of free-CML, bound-CML, free-CEL, and bound-CEL in the serum, kidney, skin, and brain. EBE also inhibited high AGEs diet-induced accumulation of bound-CML and bound-CEL in the uterus, ovary, stomach, duodenum, and colon. Meanwhile, EBE attenuated high AGEs diet-induced accumulation of free-CML and free-CEL in the muscle, bone, joint, and eyes. In addition, EBE ameliorated high AGEs diet-induced accumulation of free-CML and bound-CML in the liver, free-CML in the ovary, and bound-CML in the thyroid gland. EBE had no effect on the accumulation of free-CML, bound-CML, free-CEL, and bound-CEL in the adrenal gland and free-CML and free-CEL in the heart caused by a high AGEs diet. We did not observe AGEs accumulation in the pancreas, aorta, lung, spleen, and adipose tissues. This study revealed the in vivo distribution of CML and CEL exposed to a high AGEs diet and the effect of EBE on reducing the accumulation of CML and CEL in the specific target tissues.