Inequality in education is a challenge that have persisted and still likely to persist for a long time in the field of education because students come into the classroom with different characteristics thus posing a great concern to the realization of classroom objectives. The use of adequate teaching strategy might break this limitation thereby making every student to engage in meaning learning. The two objectives of this study include (1) to investigate the effect of brain-based teaching (BBT) method on students' retention on the topic, heat energy (2) to investigate if self-efficacy influence physics students' retention on the topic, heat energy, when taught using brain-based teaching method. We adopt the design, pre-test post-test control group quasi experimental design for the investigation. The participants were 99 (experimental group, n= 46; control group, n=53) students and were selected from two schools in Ondo using random sampling technique. A researcher designed data collection tool titled heat energy test (HET) was used to collect data in this study. HET's validity was achieved by giving the draft to three science education experts and two secondary school physics teachers for validation. Both descriptive and inferential statistics (Mean, t-test. ANCOVA) were used for analysis. Brain-based teaching method significantly improved the retention of students in physics (heat energy) and also, self-efficacy did not influence physics students' retention in physics (heat energy). In conclusion, brain-based teaching method enhanced the retention of physics (heat energy) thus breaking the limitation posed by differences in the characteristics of the students.