The aim of this study is to examine the effect of motivation, attitude, and self-efficacy beliefs of secondary school students towards science course on their academic achievement. The relational survey model was used to conduct the study. A total of 635 students, 319 females, and 316 males participated in the study. “Motivation Scale for Learning Science”, “Self-Efficacy Scale for Science”, “Attitude Scale for Science Course” were used as data collection tools. In the study, independent t-test was used to make comparisons in terms of gender, and path analysis using structural equation modeling principles was conducted to determine the direction and level of the relationship between the variables. In the results of the research, significant differences were found in students’ attitudes, motivation, and self-efficacy in terms of the gender variable. It was concluded that students’ attitudes and motivation directly affect their academic achievement. There was a strong positive relationship between attitude and motivation, a low positive relationship between self-efficacy and attitude, and a moderate positive relationship between self-efficacy and motivation. In line with the results of this research, and considering the direct effects of academic achievement on students’ motivation in science course, it is recommended that necessary information and training activities be provided to teachers in order to carry out studies on increasing students’ motivation.