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Brain trauma leads to the induction of neural stem cell proliferation and the migration of young neurons to injured areas. However, these neurons are insufficient to fully restore neuronal function due to the limited potential of adult neurogenesis. This study aimed to investigate the effect of hypoxia, a condition that underlines a wide spectrum of brain pathologies, on pluripotency and the capacity of stem cells to differentiate into neural progenitors. We analyzed the expression of SOX genes and microRNAs as they control a variety of cellular processes during neuronal differentiation, including cell proliferation and cell fate determination. In vitro neuronal differentiation of human embryonal carcinoma cell line NT2/D1 and induced pluripotent stem cells were used as a model system of adult neurogenesis. Cobalt chloride was used to induce hypoxia. The results of the analysis showed that, following hypoxia, the efficiency of neuronal induction was significantly decreased, that coincident with decline in mRNA expression levels of SOXB and SOXC genes. In contrast to that, the expression level of miR-21 was significantly increased. Our findings advance the study of SOX TFs, miR-21, and their possible interplay in ischemia-related pathologies, establishing them as prospective biomarkers and possible targets for future diagnostic and therapeutic approaches.