The learning model should be able to improve student's learning abilities. The Brain-Based Whole Learning (BBWL) model is one of the alternative learning models that can improve students' retention achievement, supported by scientific literacy and concept mastery. This study aims to determine the effect of the BBWL model on students' scientific literacy, concept mastery, and retention. This research method was quasi-experimental, with a sample of four classes taken randomly. The total sample was 132 students in grade XI Science Specialization in Madrasah Aliyah Bengkulu who enrolled in Biology. The data were analyzed using the ANOVA test after the assumption test was carried out, namely the normality and data homogeneity test. The results showed an effect of the BBWL model on students' scientific literacy skills, concept mastery, and retention. There is a significant difference between the BBWL model with BBL, WBT, and control. Based on the study results, it can be concluded that the BBWL model can improve students' retention achievement by supporting the result of good scientific literacy and concept mastery.