Purpose Cognitive training in parallel with functional near-infrared spectroscopy (fNIRS)-derived neurofeedback has been identified to be beneficial in enhancing cognitive function in patients with mild cognitive impairment (MCI). However, effects of virtual reality (VR)-based cognitive training ensuring ecological validity in parallel with fNIRS-derived neurofeedback on neural efficiency has received little attention. This study investigated effects of VR-based cognitive training in parallel with fNIRS-derived neurofeedback on cognitive function and neural efficiency in patients with MCI. Method Ninety participants were randomly assigned into the active group (AG) receiving VR-based cognitive training in parallel with fNIRS-derived neurofeedback, the sham group (SG), or wait-list group (CG). The AG and SG group performed each intervention for fifteen minutes a session, for eight sessions. The Trail Making Test Part B and Backward Digit Span Test were used for outcomes. In addition, activity in the dorsolateral prefrontal cortex (DLPFC) during cognitive testing using fNIRS was measured. Results After the eight sessions, the AG achieved greater improvements in all outcomes than the other groups. In addition, the AG showed a lower DLPFC activity during cognitive testing than the other groups. Conclusions VR-based cognitive training in parallel with fNIRS-derived neurofeedback is superior to enhancing cognitive function and neural efficiency.