The study analyzed modern e-learning and flipped classroom methods in inclusive education, focusing on their impact on motivation, academic performance, and the effectiveness of the educational process. The experiment involved 648 first- and second-year students from Abai Kazakh National Pedagogical University, the Elabuga Institute (Branch) of Kazan Federal University, and I.M. Sechenov First Moscow State Medical University. According to the survey conducted in the first phase, 66% of students reported using e-learning and flipped classroom methods, while 34% indicated that these methods were not employed. Furthermore, 50% of respondents rated the development of these methods in their universities as low, suggesting a lack of attention, familiarity among teachers, or reluctance to adopt them. To study the psychopathology of language and cognitive functions among children with special needs, the authors used the ASEBA questionnaire algorithm. It allowed for a survey among children from specialized classes, mixed classes (E-learning and flipped classroom), and control classes. Each group consisted of 50 people, there were three classes in each category. The ASEBA questionnaire revealed information about various aspects of the psychological functioning of children, including their behavior, emotional state, social adaptation, as well as problems with language and communication. The use of the questionnaire in different types of classes helped to compare the results between groups and identify features and differences in the psychopathology of language and cognitive functions in children with special needs. The findings can contribute to a deeper understanding of the psychopathology of language and cognitive functions in this category of children.