This research aims to guide teachers in designing and conducting science lessons for junior high school students. The 5E model was revised to create a five-step teaching procedure suitable to natural science characteristics. The lesson plans contain learning activities and assessment tools to measure students’ learning outcomes based on science competence criteria that students need to develop. A sample project of the Sixth Grade curriculum was planned and conducted in three classes with more than one hundred students. The qualitative (interview) and quantitative data (marks) collected after the experiments showed the interest and concentration of students in the lessons. Moreover, the data also proved the reliability and validity of assessment tools used in each 5E activity to assess students’ science competence. The results indicated the effectiveness of the 5E model in helping students practice and nurture competence in teaching natural science.