This research investigated the impact of Brain-Based Professional Development (BBPD), which utilizes theories and key findings from educational neuroscience, on shifting EFL novice teachers' pedagogical perceptions and practices. A mixed-methods research design was utilized to allow triangulation of data and explore the multi-dimensional nature of teachers' perceptions. The participants included nine novice teachers of English language enrolled in the professional diploma of curricula and methods of teaching at the Faculty of Education, Port Said University. They were tested before and after the brain-based treatment that aimed at educating teachers about brain-based learning and brain-compatible instructional practices. Teachers were encouraged to transfer the knowledge gained from the BBPD by creating brain-compatible lesson plans and developing training sessions. The instruments included two adopted questionnaires, interviews, lesson plans, and training session templates. Results emphasized the significance of BBPD in shifting EFL novice teachers' pedagogical perceptions to be more brain-compatible and student-centered. Additionally, the teachers managed to develop lesson plans that are substantiated by brain research by incorporating the principles of Brain-Based Learning (BBL) and elements of Brain-Compatible Teaching (BCT) into their lesson plans. These changes in lesson planning demonstrated efficient understanding of BBL. Besides, educational implications for successful brain-compatible pedagogy and effective EFL teachers' preparation and training programs were provided. Orchestrated efforts from the Ministry of Education (MOE), curriculum developers, teacher educators, and EFL teachers of the English language are recommended.