MicroRNAs (miRNA) are small noncoding RNAs that play important roles in cell development, differentiation and apoptosis. Recent studies showed that transmembrane protein 59 (TMEM59) affects neural stem cell (NSC) differentiation and β-amyloid precursor protein (APP) glycosylation. In this study, we predicted that microRNA-351 (miR-351) could target TMEM59 and demonstrated that miR-351 negatively regulates TMEM59 expression in different cell types. Moreover, we found that miR-351 overexpression could lead to morphological change in the mouse NSC cell line C17.2, indicating an important role of miR-351 in the regulation of differentiation. Our investigations focused on the functions of miR-351 in the nervous system and the posttranscriptional regulation of TMEM59 by microRNA. These original findings provide promising grounds for future in-depth research into the functions of miR-351 and TMEM59 in nervous system development.