The article presents the results of a study of the relationship of psychophysiological characteristics with indicators of the autonomic regulation of the body of adolescents studying in an innovative educational institution of a boarding type. The article shows that, compared with boys, adolescent girls had a lower level of visual-motor response, functional mobility of nervous processes, and brain performance. Correlations between heart rate variability indicators reflecting sympathetic influences on the heart rhythm and the level of functional mobility of nervous processes have been established. And negative connections were established with the performance of the brain, indicating the predominance of the parasympathetic activity of the autonomic nervous system in adolescents with a high level of functional mobility of nervous processes and the performance of the brain. Adolescents with a low level of neurodynamic characteristics differed from their peers in the deterioration of cognitive indicators and the functional state of the body, poor adaptation.