This research examined whether incorporating learning progress (LPs) in teaching can help Japanese lower-secondary school students systemically understand science concepts. A teaching plan incorporating the learning progressions (LPs) concept was developed. Next, a lesson was conducted for 36 third-year students of a public lower-secondary school in Japan (Hiroshima Prefecture) from the unit of “Ions and Atoms.” Then, the portfolios used in the class and the assessment questions after the class were analyzed. The results show that some students understood the concepts systemically at the grade level indicated by the LPs; however, some students did not. The results of this study suggest the following: (1) teachers should examine the appropriate teaching methods in the target unit and incorporate teaching to allow students to engage with what they are learning; (2) students should understand the lower-level concepts related to the target unit based on LPs, and if the level of understanding is insufficient, teachers should incorporate time to review and reconstruct the concepts. Keywords: lower-secondary school science, scientific concepts, learning progressions (LPs), systemic learning