Programmed exercise interventions modulating both physical fitness and cognitive functions have become a promising tool to support healthy aging. The aim of this experiment was to determine the effect of a 12-week judo training (JEX) on cognitive processing and muscle function among the elderly. Forty participants were divided into two groups: the JEX group and the control group (CTL). Before and after 12-week of JEX, participants performed a battery of physiological and psychological tests. The peripheral level of brain-derived neurotrophic factor (BDNF) was analyzed. A 12-week JEX intervention led to improved Stroop performance reflected by a shortening of the response time related to Stroop “naming” interference. In addition, the peripheral concentration of BDNF was significantly increased following the JEX compared with the CTL group. In response to JEX, balance and lower limb strength significantly increased. The current results suggest that JEX could have beneficial effects on cognitive functions, denoted by elevated peripheral BDNF, as well as on balance and strength abilities. A combination of positive effects with respect to movement and cognition makes JEX an ideal preventive lifestyle modification for the aging population.