Although it is known that brain-derived neurotrophic factor (BDNF) plays a critical role in neuronal survival and differentiation, its effect on lipid homeostasis is poorly understood. To understand them, we here investigated the effect of BDNF on the fatty acid composition of primary neurons. A detailed analysis of the fatty acid composition of BDNF-stimulated primary neurons revealed that BDNF treatment led to a significant and selective increase in intracellular palmitoleic acid (PLO) levels. Correspondingly, BDNF induced the expression of the enzyme responsible for PLO synthesis [stearoyl-CoA desaturase-1]. In addition, this increase was suppressed by K252a, an inhibitor for tropomyosin-related kinase (Trk) receptors, indicating that BDNF-dependent increase in the PLO was mediated through the activation of TrkB. Further, PLO in culture media was reduced by BDNF treatment. This result suggested that BDNF suppressed extracellular release of PLO. Taken together, these data indicate that BDNF increases intracellular PLO both by activating its biosynthesis and by suppressing its extracellular release.