Metabolic dysregulation of neurons is associated with diverse human brain disorders. Metabolic reprogramming occurs during neuronal differentiation, but it is not fully understood which molecules regulate metabolic changes at the early stages of neurogenesis. In this study, we report miR-124 as a driver of metabolic change at the initiating stage of human neurogenesis. Proteome analysis has shown the oxidative phosphorylation pathway as the most significantly altered among the differentially expressed proteins (DEPs) in the immature neurons after the knockdown of miR-124. In agreement with the proteomics results, miR-124 depleted neurons displayed mitochondrial dysfunctions, such as decreased mitochondrial membrane potential and cellular respiration. Moreover, morphological analyses of mitochondria in early differentiated neurons after miR-124 knockdown resulted in fragmented shapes. Lastly, we showed the potential of DEPs as metabolic regulators in neuronal development by validating the effects of GSTK1 on cellular respiration. GSTK1, upregulated most significantly in miR-124 knockdown neurons, reduces oxygen consumption rate of neural cells. Collectively, our data demonstrate and emphasize the roles of miR-124 in coordinating metabolic maturation at the early stage of neurogenesis.