The purpose of this study is to examine teachers’ and students’ perceptions and practices in the teaching- learning process of science and mathematics subjects. It also seeks to explore the contribution of teachers perception to the practice of effective teaching, examine whether there is difference in practicing effective teaching between male and female teachers or not, identify the practice of teaching Science and Mathematics and explore the presence of difference on teachers’ perceptions (based on subject matter teaching and teaching experience) to effective teaching-learning process of Sciences and Mathematics subjects. The study was complemented by mixed method approach with a convergent parallel or concurrent mixed methods design. The researcher collected data from teachers and students by moving door-to- door and in their schools using available sampling techniques. The sample included a total of 60 teachers and 20 students). Questionnaires and interviews are employed to collect data. The quantitative data was analyzed by using frequency, percentage, liner regression, independent t- test and one way -ANOVA and the qualitative data was analyzed in organizing, summarizing and interpreting narrative description way. The results reveal that perceptions are the most contributor variable to the practice of effective teaching. However, the practice of teaching Science and Mathematics subjects were not implement effectively. No significant differences were found between male and female teachers in their practice of effective teaching. However, the analysis of one way –ANOVA revealed that except mathematics teachers no significant difference was found in perceptions on effective teaching in terms of years of experience. Finally, it is recommended that to convey the practice of effective teaching of Science and Mathematics education teachers, students, government, society and industry should be in a co-operation and work together.