Many educational researchers have investigated how best to support conceptual learning in science education. In this study, the aim was to design learning materials using Physlets, small computer simulations, and to evaluate the effectiveness of these materials in supporting conceptual learning in secondary school physics. Students were taught in two different physics courses (conditions): one group of students (n = 40) was taught using Physlet-based learning materials, and the other (n = 40) was taught using expository instruction. To evaluate the designed materials, we assessed students' thinking skills in relation to physics after the course and analyzed the results using an independent t test, multiple regression analyses, and one-way analysis of covariance. The results showed better thinking skills among students in the experimental group and supported a clear relationship between the physics course using Physlet-based materials and this improvement (p < 0.05). These results indicate that properly designed Physlet-based materials can effectively support conceptual learning.