Background: Despite the neurotrophins like brain-derived neurotrophic factor and insulin-like growth factor-1 are thought to have important role in neurorehabilitation, the factors that affect these biomarkers are not well known. Objectives: We aimed to investigate the effect of maximal aerobic exercise on serum neurotrophins levels in patients with chronic stroke and to investigate the factors that affect their resting and exercise-associated levels. Patients and Methods: Potential factors of resting and exercise-related serum neurotrophins levels were studied among 35 patients with chronic stroke. Resting brain derived neurotrophic factor, resting insulin-like growth factor, exercisedependent change brain derived neurotrophic factor, and exercise- dependent change in insulin-like growth factor were studied using demographic, disease burden, and cardiometabolic factors. Results: Brain-derived neurotrophic factor did not change after exercise (p = 0.38) while insulin-like growth factor decreased (p = 0.001). Higher resting brain-derived neurotrophic factor was determined by greater lower extremity impairment (p = 0.004, r2 = 0.23). The greater response of brain-derived neurotrophic factor to exercise was determined by higher fluid intelligence (p = 0.01, r2 = 0.18). Resting insulin-like growth factor-1 was not changed by all of the studied factors. Conclusion: Resting and percent change in brain-derived neurotrophic factor were associated with cognitive and physical recovery after chronic stroke. On the other hands, insulin-like growth factor-1 was not useful in chronic stroke. Interestingly, fluid intelligence was positively associated with exercise-related rise in brain-derived neurotrophic factor.