The article considers the possibilities of motivation education for pupils with special educational needs while studying the subject of natural cognition. As the Ministry of Education, Science and Sport of the Republic of Lithuania states, the majority of pupils with special educational needs are educated at general education schools together with their peers through inclusive education. STEM method is best suited for pupils with special educational needs due to the integration of the pupils in the curriculum with the whole class, allowing them to choose tasks. In order to highlight how to strengthen the learning motivation of pupils with special educational needs, qualitative research is chosen. During the qualitative research, a structured interview is conducted, the data of which is processed by the content analysis method. The study included 7 pupils with special educational needs. Interviewed pupils indicate, that their learning motivation is influenced by good relationships a pupil – a pupil, a teacher – a pupils, a parent – a pupil; possibilities to work in a group; variety of learning environment (e.g. outdoor class); discussion of successes and failures, highlighting progress.