Systems and methods for transfection using a microfluidic device are disclosed. Microdroplets encapsulate cells, transfection molecules, and cationic lipid transfection reagent. Droplet chaotic advection in a rendering channel of the system results in a uniform lipid-DNA complex (lipoplex) formation, which can improve gene delivery efficacy. The shear stress exerted on cell membranes during the chaotic mixing increases membrane permeability, which when combined with the co-confinement of cell and lipoplex, improves transfection efficiency of the cell. The systems and methods can be used for a variety of applications such as gene therapy, in vitro fertilization, regenerative medicine, cancer treatment, and vaccines.