The study focused on the Effect of utilizing Brain-based learning design to the self-efficacy and outcomes of the students in science classroom. The researcher surveyed 167 Grade 8 students whom the data needed to identify that the level of brain-based learning design, level of students’ self-efficacy, level of students’ written output, level of students’ performance output and influences brain-based teaching approach students' self-efficacy and contribute to their academic outcomes in the science classroom. The study utilized concurrent mixed method research design. The main instrument that will be use is a researcher-made questionnaire checklist in the form of multiple-choice test to gather the needed data and semi structured interview questionnaire. The respondents of the study are one hundred sixty-seven (167) Grade 8 students of Pedro Guevara Memorial National High School for quantitative data while 6 participants were included to obtain. The statistical tools used were mean, standard deviation and quantile regression was used to test the hypothesis. From the procedure recapitulated from above, the basic questions were solved. Based on the results of the data, the findings were drawn from this study. The implementation of brain-based teaching approach in science were very high in terms of spaced repetition, generative learning, reproducing information, and chunking. Students attained very high perception on their capacity upon integration of brain-based learning design in the teaching and learning process. Most of the students were classified as Fairly Satisfactory, some Did not meet expectation and only few of them are showed satisfactory in written output in terms of diagnostic assessment while most of the respondents are very satisfactory, some are satisfactory and others attained outstanding performance in written output in terms of summative. Also, Most of the students showed outstanding level of students’ performance output terms of Practical Test while there are only few who are classified as very satisfactory. Furthermore, the brain-based learning design were viewed by the learners as effective learning design for science subject as it enhance their competency, efficacy and learning experiences. In line with the findings of the study it can be concluded that there is significant effect in utilizing brain-based learning design to the students’ self-efficacy. Thus, the posited null hypothesis is rejected. Denoted that the brain based learning design aids the development of student’s self-efficacy. While, finding show that utilizing design approach has no significant effect in to the students’ outcomes thus the posited null hypothesis stating that There is no significant effect in utilizing teaching approach to the students’ outcomes is sustained. Based on the conclusions laid, it is recommended that schools are suggested to promote brain-based learning for complex topics, share best practices among teachers, involve students in goal-setting, use interactive methods to boost participation and confidence, identify learning styles, and use interactive activities to enhance learning experiences. Future research should explore how students adapt brain-based methods in their study habits and how it affects their academic performance.