Electroporation technique has recently emerged as a tool for delivery of foreign molecules into cells. However, the electroporation has many critical hurdles to overcome in cell viability, delivery efficiency, and productivity. To overcome the hurdles with a single platform, we devised a polyimide (PI) film-based on- chip electroporation system that shields the cells from the electrodes with four sheath flows, enabling a 3D flow focusing. This on-chip electroporation with a double forced-flow (OE-DFF) configuration enhances the cell viability to such an extent that even with a long spiral channel for high molecular delivery efficiency, which is detrimental to the cell viability due to longer exposure to the electric field, the cell viability is still increased substantially. The advantages provided by the OE-DFF system is demonstrated with a fluorescent probe molecule (FITC-BSA) and pPtCrCFP plasmid delivered into Chlamydomonas reinhardtii, one of the challenging cell lines to transform. The continuous nature of the flow system assures high throughput. This novel approach in microfluidic science is expected to greatly contribute to algal research as an efficient electroporation tool as well as to broad applications.