This research describes the application of Challenge Based Learning to STEM students. The overall goal is to identify the effectiveness of challenge-based learning in developing some analytical thinking skills among students of STEM education program in the faculty of Education. To achieve this goal, the current research sought to answer the following main question: What is the effectiveness of challenge-based learning in developing some analytical thinking skills of STEM students in the faculty of education? The researcher prepared research materials and tools represented in the suggested program of biotechnology in the light of Challenge based learning and analytical thinking skills test.  The experimental approach was used, the quasi-experimental design with one experimental group, and the research was applied on a group of first year STEM students at the Faculty of Education, Zagazig University, their number was 30, and the following results were reached: There is a statistically significant difference at the significance level (0.01) between the mean scores of the experimental group students in the pre- test and posttest of the analytical thinking test as a whole and in its sub-skills in favor of the posttest. There is an effectiveness of challenge-based learning in developing some analytical thinking skills among STEM students in the Faculty of Education.