This study explores whether the context-based approach with 5E model (CBA-5E) can lead to better understanding of chemical reactions and energy concepts when compared to conventional instruction (CI). Additionally, the study delves into the effect of treatment with regards to gender. Eleventh grade science-major classes with 175 students from two public high schools were enrolled. The experimental groups were treated with CBA-5E, the control groups as CI, the treatments were randomly assigned to the groups. The chemical reactions and energy concepts test, including the common alternative conceptions, was administered as pre- and post-test. The chemical reactions and energy achievement test, including conceptual and algorithmic problems, was administered as a post-test to the groups. Multivariate Analysis of Covariance (MANCOVA) was used for the analysis of the data, and the results revealed that CBA-5E was superior to CI on the students' conceptual understanding regarding these concepts regardless of gender difference.