Genetic approaches to control DNA expression in different brain areas have provided an excellent system to characterize gene function in health and disease of animal models. With respect to others, in utero electroporation of exogenous DNA into progenitor cells committed to specific brain areas is the optimal solution in terms of simplicity and velocity. Indeed, this method entails one quick and easy surgical procedure aimed at DNA injection in the embryonic brain followed by brief exposure to a strong electric field by a bipolar electrode. Nevertheless, the technique is still lacking the necessary control and reliability in addressing the field. Moving from a theoretical model that accounts for the morphology and the dielectric properties of the embryonic brain, we developed here a set of novel and reliable experimental configurations based on the use of three electrodes for electroporation in mouse. Indeed, by means of a full 3D model of the embryonic brain and the surrounding environment, we showed that the distribution of the electric field can be finely tuned in order to target specific brain regions at a desired temporal window by proper placement of the three electrodes. In the light of this theoretical background, we manufactured a three-electrode device and performed model-guided experimental sessions. The result was an increased spatial control, extended time frames and unprecedented reliability of the genetic manipulation, with respect to the current state of the art. In particular, the outcomes of this method applied into the mouse model are reported here for the first time.