The present invention relates to a method of forming junctions of a semiconductor device. According to the method of forming junctions of a semiconductor device in accordance with an aspect of the present invention, there is provided a semiconductor substrate in which a transistor including the junctions are formed. A first thermal treatment process for forming a passivation layer over the semiconductor substrate including the junctions is performed. Here, the passivation layer functions to prevent impurities within the junctions from being drained. A pre-metal dielectric layer is formed over the semiconductor substrate including the passivation layer.