Multimedia technology is now growing rapidly, one of the areas that get a significant impact in the development of this technology is the field of education. In the teaching-learning process in MTs N 25 still using the one-way transfer knowledge system to place students as an object and as a subject teacher. This makes the students tend to be passive and less showed a level of creativity in the process of transfer of knowledge from material provided by the teacher to the student learners. Learning process in one direction only educates students listen describe it, so that not infrequently lead to boredom in the classroom. Learning environment such as this will make it difficult for students to understand and accept the material provided by the teacher. Thus the concept of learning methods with the use of interactive multimedia technology to answer these problems, because the multimedia learning with interactive animation to support the learning process by creating a pleasant atmosphere in the process of learning, so that students are easy to understand and accept the material provided. The design of interactive animated multimedia-based learning brain anatomy created using macromedia flash 8, while the analysis is the whitebox testing, region, matrix graphics, blackbox testing, and analysis of questionnaires with mathematical models through simple tabulation method.