This study has demonstrated the optimization of an electroporation (EP) system for gene transfection by using the Taguchi method. The parameters of the EP system, which could have an influence on the transfecting rate, were optimized, resulting in values of 50 μm electrode gap, 80 μg/mL pEGFP-Nl concentration, 6 V pulse voltage, and 2-pulse. A larger-the-better Ω transformation was employed for better additivity. The analyzed results of interaction A × C, A × D, and C × D showed that there were strong interactions on level 3 of factors A, C, and D to each others. Using optimized EP system, the pEGFP-Nl plasmid was successfully transfected into the basal cell carcinoma cell line (BCC) with 40.36% average transfecting rate.