The purpose of the current study was to explore various behavioral and neuroelectric indices after acute aerobic exercise in young adults with different cardiorespiratory fitness levels when performing a cognitive task, and also to gain a mechanistic understanding of the effects of such exercise using the brain-derived neurotrophic factor (BDNF) biochemical index. Sixty young adults were separated into one non-exercise-intervention and two exercise intervention (EI) (i.e., EIH: higher-fit and EIL: lower-fit) groups according to their maximal oxygen consumption. The participants' cognitive performances (i.e., behavioral and neuroelectric indices via an endogenous visuospatial attention task test) and serum BDNF levels were measured at baseline and after either an acute bout of 30min of moderate intensity aerobic exercise or a control period. Analyses of the results revealed that although acute aerobic exercise decreased reaction times (RTs) and increased the central Contingent Negative Variation (CNV) area in both EI groups, only the EIH group showed larger P3 amplitude and increased frontal CNV area after acute exercise. Elevated BDNF levels were shown after acute exercise for both EI groups, but this was not significantly correlated with changes in behavioral and neuroelectric performances for either group. These results suggest that both EI groups could gain response-related (i.e., RT and central CNV) benefits following a bout of moderate acute aerobic exercise. However, only higher-fit individuals could obtain particular cognition-process-related efficiency with regard to attentional resource allocation (i.e., P3 amplitude) and cognitive preparation processes (i.e., frontal CNV) after acute exercise, implying that the mechanisms underlying the effects of such exercise on neural functioning may be fitness dependent. However, the facilitating effects found in this work could not be attributed to the transient change in BDNF levels after acute exercise.