Although regular Taekwondo (TKD) training has been reported to be effective for improving cognitive function in children, the mechanism underlying this improvement remains unclear. The purpose of the present study was to observe changes in neuroplasticity-related growth factors in the blood, assess cerebral blood flow velocity, and verify the resulting changes in children’s cognitive function after TKD training. Thirty healthy elementary school students were randomly assigned to control (n = 15) and TKD (n = 15) groups. The TKD training was conducted for 60 min at a rating of perceived exertion (RPE) of 11–15, 5 times per week, for 16 weeks. Brain-derived neurotrophic factor (BDNF), vascular endothelial growth factor (VEGF), and insulin-like growth factor-1 (IGF-1) levels were measured by blood sampling before and after the training, and the cerebral blood flow velocities (peak systolic [MCAs], end diastolic [MCAd], mean cerebral blood flow velocities [MCAm], and pulsatility index [PI]) of the middle cerebral artery (MCA) were measured using Doppler ultrasonography. For cognitive function assessment, Stroop Color and Word Tests (Word, Color, and Color-Word) were administered along with other measurements. The serum BDNF, VEGF, and IGF-1 levels and the Color-Word test scores among the sub-factors of the Stroop Color and Word Test scores were significantly higher in the TKD group after the intervention (p < 0.05). On the other hand, no statistically significant differences were found in any factors related to cerebral blood flow velocities, or in the Word test and Color test scores (p > 0.05). Thus, 16-week TKD training did not significantly affect cerebral blood flow velocities, but the training may have been effective in increasing children’s cognitive function by inducing an increase in the levels of neuroplasticity-related growth factors.