The purpose of this study was to determine the mediating effect of science learning environment on the relationship between student academic motivation and self-efficacy of senior high school student of Baganga North District Division of Davao Oriental, Region XI, Philippines. The study utilized a quantitative, non-experimental design via correlational technique and mediation analysis.Futhermore,204 senior high students respondents were survey using universal sampling an adapted 5 point likert scale survey questionnaires. Weighted, mean, Pearson r, and multiple regression were used as statistical tools. Moreover, all of the three variables obtained a high level and revealed a significant relationship between student academic motivation and self-efficacy, there was a significant relationship between science learning environment and student academic motivation and a significant relationship between science academic motivation and self-efficacy of senior high school students, three variables. Furthermore, science learning environment has a partial mediating effect on the relationship between student academic motivation and self-efficacy of students in science. This means that the science learning environment influences the strength of the relationship between the student academic motivation and self-efficacy.