Purpose This study examined the effect of 12 weeks of concurrent aerobic and resistance training on brain derived neurotrophic factor (BDNF) levels, neuromuscular performance and cerebral oxygenation on self-paced cycling exercise in previously untrained older men. Methods Eight untrained healthy males aged 53–64 years performed a familiarisation and a pre-training self-paced cycling time trial before 12 weeks of exercise training which combined aerobic and resistance exercise. The self-paced cycling time trial comprised a 30 s maximal effort sprint for every 4.5 min of lower intensity pace for a total of 25 min. Upon completion of 12 weeks of training, a comparison of the pre-training trial analysed for serum BDNF, neuromuscular performance, and cerebral oxygenation was undertaken. Results Serum BDNF decreased significantly from 10.02 ± 4.63 to 6.96 ± 3.56 ng/ml after 12 weeks of training. There was also attenuated physiological strain for a comparable self-paced cycling performance. Despite positive physiological responses during the time trial pacing strategy was not altered compared with pre training. Conclusion BDNF decreases following 12 weeks of concurrent training and might reflect neuroplasticity for this type of training stimulus. Exercise training in previously sedentary older men can result in a multitude of physical benefits, which may also confer a neuroprotective effect. However, specific training is required to improve pacing strategies in previously untrained older males. Clinical trial registration Australian New Zealand Clinical Trials Registry number ACTRN12622001477718 .