This study was aimed at investigating the effect of lesson study on science teachers’ Pedagogical Content Knowledge and Self Efficacy. This study was conducted at three public junior high schools in Singaraja city. There were nine teachers who participated in this study. They had worked for more than 10 years. They did lesson study activites in three cycles, each cycle consisted of planning, action, and reflection. The data were collected by using pedagogical content knowledge test with the reliability index r= 0.71 and self efficacy questionnaire with the reliability index r= 0.92 .The data were analyzed descriptively using normalized gain score (g) formula. The results indicated that lesson study can improve science teachers’ pedagogical content knowledge and self efficacy. Through lesson study the teachers could get the opportunity to plan the instruction collaboratively, observing the instructional practice well, doing a reflection, and improving the instruction. The result of this study implies that schools need to provide opportunities for the teachers to do lesson study periodically.