The article presents the studying of psychophysiological adaptation features results of primary school age pupils, enrolled in innovative educational institution. Comprehensive survey of elementary school students, which was held during two years of study (the first to the second year of study), presupposed a research of psychophysiological indicators and assessment of the regulatory systems of the body. It was found that by the second year of study the students are improving developmental quotient of cognitive performance by increasing the pressure in the cardiovascular system regulation. Those students who had low performance indicators in the beginning of the education program showed more prominent dynamics of psycho-physiological functions during the two years of study, compare to their peers with ‘good" or "excellent" marks. The boys had greater dynamics in the amount of attention compared to girls. Adaptation process of students with high academic performance, accompanied by increased sympathetic activity in heart rate regulation, is accompanied by a greater physiological "cost" that the body pays for the effectiveness of implemented activities.