Two-layer microfluidic devices with porous membranes have been widely used in bioapplications such as microphysiological systems (MPS). Porous electrodes, instead of membranes, have recently been incorporated into devices for electrochemical cell analysis. Generally, microfluidic channels are prepared using soft lithography and assembled into two-layer microfluidic devices. In addition to soft lithography, three-dimensional (3D) printing has been widely used for the direct fabrication of microfluidic devices because of its high flexibility. However, this technique has not yet been applied to the fabrication of two-layer microfluidic devices with porous electrodes. This paper proposes a novel fabrication process for this type of device. In brief, Pluronic F-127 ink was three-dimensionally printed in the form of sacrificial layers. A porous Au electrode, fabricated by sputtering Au on track-etched polyethylene terephthalate membranes, was placed between the top and bottom sacrificial layers. After covering with polydimethylsiloxane, the sacrificial layers were removed by flushing with a cold solution. To the best of our knowledge, this is the first report on the sacrificial approach-based fabrication of two-layer microfluidic devices with a porous electrode. Furthermore, the device was used for electrochemical assays of serotonin and could successfully measure concentrations up to 5 µM. In the future, this device can be used for MPS applications.