This study investigated the effects of acute aerobic exercise on neuropsychological and neurophysiological performances in young adults with different cardiorespiratory fitness levels when performing a task-switching protocol and explored the potential associations between acute aerobic exercise-induced changes in serum brain-derived neurotrophic factor (BDNF) concentrations and various neurocognitive outcomes. Sixty young adults were categorized into one control group (i.e. non-exercise-intervention; n = 20) and two exercise-intervention (EI) groups [i.e. higher (EIH, n = 20) and lower (EIL, n = 20) cardiorespiratory fitness] according to their maximal oxygen consumption. At baseline and after either an acute bout of 30 min of moderate-intensity aerobic exercise or a control period, the neuropsychological and neurophysiological performances and serum BDNF concentrations were measured when the participants performed a task-switching protocol involving executive control and greater demands on working memory. The results revealed that although acute aerobic exercise decreased reaction times across three (i.e. pure, switching and non-switching) conditions in both EI groups, only the EIH group showed a smaller switching cost and larger P3 amplitudes after acute exercise, supporting the view that the mechanisms of neural functioning that underlie the effects of such exercise may be fitness dependent. In addition, serum BDNF concentrations were elevated after acute exercise for both EI groups, but there were no significant correlations between the changes in BDNF concentrations and changes in neuropsychological and neurophysiological performances for either group, suggesting that serum BDNF could not be the potential factor involved in the beneficial effects on neuropsychological and neurophysiological performances seen in young adults after acute aerobic exercise.