This study focuses on the design and experimental verification of an electroporation (EP) microchip system for the transfection of zebrafish (Danio rerio). For generating suitable pulses, a circuit is used to provide voltages between 0 and 700 V, with nearly 0-3,500 V/cm electric field. In addition, a proposed EP microchip, designed in a modular fashion, is fabricated using micro electromechanical system (MEMS) technology to allow for rapid and convenient replacement of each component. A numerical simulation is carried out to analyze the uniformity and strength of the EP electric fields generated in the microchip. Trypan blue dye, water-soluble quantum dots (MUA-QDs) and genes coding for green fluorescence protein (pEGFP-N1 plasmids) were employed to verify the successful delivery and transfection of zebrafish embryos. The experimental results show that the optimum delivery rate of trypan blue dyes and MUA-QDs were respectively up to 62 and 36% by using the proposed EP system. The successfully transfected embryos with the pEGFP-N1 plasmid used exhibit green fluorescence in the zebrafish embryos. The approach in the transfection of zebrafish embryos will provide many potential usages for cellular imaging areas, gene therapy research and medical applications.