Children with special educational needs (SEN) not associated with disabilities are those who have difficulty accessing common learning according to their age. To support these children, the curriculum is adapted according to the level of competence they develop, including specific resources to improve their teaching-learning process. For this reason, the electronic pedagogical assistance system for children with special educational needs using augmented reality was implemented to facilitate the learning of content in a visual and auditory manner. This system was developed emphasizing the suggestions provided by teachers, psychopedagogues, and the psychopedagogical report that this group of students possesses. The application makes use of 3D models and interactive videos specifically designed for Natural Sciences topics. By recognizing specific markers, the application executes image detection and tracking processes through the Unity 3D graphics engine and the ARCore SDK. Additionally, descriptive audios and environmental sounds are played to enhance the educational experience. Students interact with the system through a prototype pen that allows them to point to each auditory resource, enabling communication with the Arduino Mega development board to execute dynamic and adaptive feedback on the learned content. This innovative approach not only improves students’ attention and concentration but also increases their academic performance, demonstrating an important milestone in educational inclusion through the use of new technologies.