An efficient protocol for the synthesis of 2-aryl-5-benzylpyrimidine-4,6-diamines from readily available substituted 2-benzylidenemalononitriles and substituted benzamidines was developed. This practical protocol provided high value pyrimidine-4,6-diamines in moderate to good yields under simple reaction conditions. This approach also enables some modifications of structurally complex bioactive molecules which exhibits potential applications in medicinal chemistry.