The current study aimed to explore the effect of Brain-Based Learning on students' intrinsic motivation (IM) to learn and perform in mathematics. Owing to the educational implications of Neuroscience, the researchers planned the mixed-methods experimental study with a convergent parallel research design. The participants were eighth-graders enrolled in a boy's public secondary school in the district Kasur of Pakistan in the academic year 2021-2022. Students were taught mathematics using the traditional lecture method in the baseline phase (A) and withdrawal phase (A). In contrast, in the treatment phase (B), they were taught mathematics with activities based on the BBL approaches and principles. The mathematics motivation scale and observation (field notes) were used to collect quantitative and qualitative data simultaneously. Data were analysed using one-way repeated measure ANOVA and thematic analysis. The researchers revealed that BBL significantly affects students' IM to learn and perform in mathematics. After qualitative analysis, it was found that visual story-telling, role-playing, i-Think maps, back-to-board, and Kick Me Poison Box are the most effective BBL-based activities which keep them engaged, provide emotional support and contribute to students' IM to learn and perform in mathematics. The teachers were suggested to develop BBL-based activities to teach mathematics and to influence students' psychology in the schools.