Mathematics learning in elementary schools is still dominated by conventional methods in explaining the material in class, thus less supporting the development of critical thinking skills. This challenge is increasingly relevant to 21st-century learning and the Merdeka Curriculum, which demand the integration of technology and critical thinking skills in the learning process. This study aims to describe the influence of brain based learning assisted by PhET Simulation on the critical thinking skills of elementary school students. The method used was quasi-experimental with a non-equivalent control group design. The sample consisted of 147 elementary school students in Magelang Tengah District, Magelang City. The study was conducted in May–June 2025. Students were given a mathematics critical thinking skills test before (pretest) and after (posttest) the implementation of brain based learning assisted by PhET Simulation. Data were analyzed using an independent sample t-test to measure the influence and the N-Gain test for effectiveness. The results of the independent sample t-test analysis showed a sig value of 0.00 < 0.05, indicating a significant influence of brain based learning assisted by PhET Simulation on students’ critical thinking skills. The N-Gain test showed an average of 0.5002, which means that brain based learning is categorized as moderate or quite effective in improving students’ critical thinking skills. These findings indicate that the integration of BBL and PhET Simulation is effective in improving the quality of mathematics learning in elementary schools. Implikasi penelitian ini menunjukkan bahwa Brain and technology-based learning models support the Merdeka Curriculum by developing critical thinking. The contribution of this research is in the form of strategic steps to develop learning to balance brain function with the help of technology to support 21st century skills.