In this paper, an answer to the problem of the synchronization between two non-identical Josephson junctions (NJJ) has been given. The NJJ system includes two junctions, which are modelled by the capacitive and nonlinear resistive components. The junctions have been coupled via a coupling resistance R-cp as a synchronization control parameter to each other and two distinct current sources drive the overall system. The system has been performed in MatLab Sintulink environment and a Wide control parameter space has been scanned in order to provide the best solution to the synchronization problem. It has been proven that the system can lead to good synchronized states, if R-cp can be adjusted sufficiently large. The error stays at the level of 10(-5) although the normal state and superconducting sub gap resistances differ much for two junctions. In addition, the gap voltages are also different and that is important to learn even that kind of a nonidentical system can lead to a good synchronization under such different parameters.