Optically induced electroporation (OIE) is a promising microfluidic-based approach for the electroporation of cell membranes. However, previously proposed microfluidic cell-electroporation devices required tedious sample pre-treatment steps, specifically, periodic media exchange. To enable the use of this OIE process in a practical protocol, we developed a new design for a microfluidic device that can perform continuous OIE; i.e., it is capable of automatically replacing the culture medium with electroporation buffers. Integrating medium exchanges on-chip with OIE minimises critical issues such as cell loss and damage, both of which are common in traditional, centrifuge-based approaches. Most importantly, our new system is suitable for handling small or rare cell populations. Two medium exchange modules, including a micropost array railing structure and a deterministic lateral displacement structure, were first adopted and optimised for medium exchange and then integrated with the OIE module. The efficacy of these integrated microfluidic systems was demonstrated by transfecting an enhanced green fluorescent protein (EGFP) plasmid into human embryonic kidney 293T cells, with an efficiency of 8.3%. This result is the highest efficiency reported for any existing OIE-based microfluidic system. In addition, successful co-transfections of three distinct plasmids (EGFP, DsRed and ECFP) into cells were successfully achieved. Hence, we demonstrated that this system is capable of automatically performing multiple gene transfections into mammalian cells.