This paper describes measurement system of membrane proteins with a rapid perfusion capability using microfluidic channels. In the previous report, we successfully recorded channel conductance of alpha-hemolysine (αHL) in bilayer lipid membranes (BLMs) using droplets contacting method with PDWC (parylene double well chip). This method is one of the easiest ways for preparing the BLMs, just pipetting droplets of the solution. The drawback of the droplet-based systems is the incapability of exchanging solution. To efficiently test the effect of inhibitors and promoters of membrane proteins in drug discovery, the solution exchange is mandatory. In this study, we proposed the concept of solution exchange in the system using microfluidic channel. We demonstrated rapid perfusion that is capable of exchanging the solution within 20 s in this droplets contacting system. We experimentally evaluated the system in terms of the flow rate and the BLM stability and demonstrated the binding assay of a membrane protein using its blockers. We believe that this method is necessary for efficient drug screening in our droplet-based system.