Improving educational outcomes requires concentrated efforts and part of the solution involves helping students to improve their critical thinking skills. This study focused on the effects of the developed harmonised learning activities in selected topics in Chemistry on the students academic performance and critical thinking skills. This quasi-experimental design involved one hundred fifty (150) junior high school students and twenty (20) science teachers from six public schools in Liliw, Magdalena and Majayjay, Laguna. The activities were carried out for three months simultaneously in the participating schools. The level of students academic performance was measured and evaluated using the mean standard deviation and T-test. Research findings showed that the level of acceptability of the harmonised learning activities in selected topics in Chemistry in terms of objectives, content, and activities are extremely acceptable. The level of performance in the experimental group has a verbal interpretation of did not meet expectation in terms of pre-test. In terms of post-test the level of students’performance in the experimental group have a verbal interpretation of very satisfactory. The null hypothesis tested at 0.05 level of significance indicated that there is a significant difference between the students performance on pre-test and post-test of the experimental group. This means that the harmonised learning activities influenced the students performance positively; it is an effective tool that enhances, improves and fortifies the critical thinking skills of the students. School administrators may encourage teachers to produce self-made instructional materials which in turn will help improve the quality of education.