Cell fusion has been widely applied in scientific research for cancer immunotherapy, antibody production, and nuclear reprogramming of somatic cells, and therefore the cell fusion technique that enable us to precisely control the fusion process with high throughput manner has been desired. Here, we present a novel microfluidic method for automatic cell pairing by microdroplets, separation of droplets containing cells, and electrofusion of cells inside a droplet. The proposed microfluidic device mainly composed of three sequential function parts for (i) encapsulation of cells into a droplet by microfluidic droplet generator, (ii) separation of droplets containing cells from empty droplets through a micropillar array, and (iii) electrofusion of cells inside the droplets by applying a voltage during the droplet passing over the pair of electrodes. In the microfluidic device, cell-encapsulated and empty droplets were generated at the upstream cross-junction; they then entered the micropillar array, separating the cell-encapsulated droplets from empty droplets continuously. After separation, they passed over the electrode pairs, and were collected the outside of the microchannel. This continuous process for cell fusion would enable us to observe and isolate the target fused cells for cell analysis.