Introduction: Brain derived neurotrophic factor (BDNF) have neuroprotective effect through binding with tyrosine kinase B (TrkB). Thus the Aim of the present study was to investigate the effects of eight weeks endurance training on BDNF and TrkB levels in the hippocampus of ischemic induced male rats. Methods: 40 Male wistar rats (12 weeks old and 228. 19± 21. 18g) were divided into four groups, including: ischemic control, ischemic training, healthy control, healthy training. To induce ischemia, carotid artery is clamped with microsurgery clamp for 45 minutes. Training groups (healthy and ischemic), trained with 30m/min (70% VO2max), 30min/day, and 5 days/week on the treadmill. BDNF and TrkB levels of the hippocampus were measured using ELISA method. For data analysis, one-way ANOVA and post hoc Tukey tests were performed at a significance level of P˂ 0. 05. Results: The results showed that BDNF levels in hippocampus of ischemic control group were significantly lower than healthy control and healthy training group (P values 0. 001, 0. 002 respectively). No significant differences were found between BDNF levels in ischemic training with ischemic control and healthy control group (p values 0. 54, 0. 091 respectively) and No significant differences were found between TrkB levels in ischemic control with healthy control and ischemic control group (p values 0. 675, 0. 821 respectively). TrkB level in healthy training group was significantly higher than healthy control, healthy training groups (P=0. 001). Conclusions: Based on these results, it seems that endurance training can have neuroprotective effect through increasing the level of BDNF and TrkB level in hippocampus of ischemic rats and can be studied as a complementary therapy in ischemic disease.