BDNF levels are reduced in the chronically stressed brain, in the area of hippocampus. Part of the hippocampal BDNF is provided by neuronal projection of the entorhinal cortex. Studying the cortico-hippocampal transport of BDNF in vivo is technically difficult. Here, we describe a protocol that reproduces mouse cortico-hippocampal circuit in vitro by plating neurons on the microfluidic devices and infecting the neurons with virus-encoding BDNF-mCherry, which allows investigation of the effects of elevated corticosterone levels on BDNF axonal transport. For complete details on the use and execution of this protocol, please refer to Agasse et al. (2020).