Telomere length is one of the key components of cell lifespan and is maintained by the telomerase reverse transcriptase (TERT), an elongation enzyme for telomere. Increased TERT activity has been reported in cancer cells, while abnormal shortening of telomere length has been reported in several diseases such as diabetes and hypertension. We also reported an abnormal shortening of telomere length in the blood and brain of suicide victims. In this study, we investigated the relationship between depression and brain telomeres using an animal model of depression. We evaluated adult rats exposed to juvenile stress as an animal model of depression. Model rats showed prolonged immobility time in the forced swimming test. Abnormal shortening of telomere length was observed in the medial prefrontal cortex and dorsal hippocampus of model rats. TERT was significantly decreased in the hippocampus of model rats. Shortening of telomere length and decrease of TERT in the hippocampus of model rats were restored by repeated administration of escitalopram. Furthermore, we found abnormal signaling of GSK3β and β-catenin, which are depression-related genes and transcriptional regulators of TERT, in the hippocampus of model rats. These results provide novel pathophysiological insights into depression.