Adolescence is characterized by increased reactivity to stress factors, among the sources of which the educational environment plays a significant role. The content of education and educational process organization, as well as interpersonal relationships, is the predominant stress factors of the educational environment. In the context of education reform, new pedagogical projects are being introduced, in particular, on the basis of meritocratic education, providing for the intensification of the educational process. It may affect the state of the autonomic regulatory systems of students. The purpose of the research is to study the activity level of autonomic regulatory systems among students of secondary school, who are studying in meritocratic and traditional gymnasium education systems. The study involved 60 students: 42 studied in meritocratic system (19 in SG-1, 23 in SG-2), and 18 in traditional system (SG-3). Heart rate variability (HRV) was used as a physiological marker of stress. ECG was recorded during 5 minutes in a darkened room in a rest state with closed eyes in a sitting position at the 5th, 6th and 7th grades. Intergroup comparisons of HRV parameters were carried out according to the Mann-Whitney, Kruskell-Wallis, Dunnett criteria, and the φ-criterion of the angular Fisher transformation. Differences were considered significant at р≤0.05. In the 6th grade, there was a tendency (0.05<р≤0.07) to lower values of Mean, SDNN, TR, ΔX, RMSSD, pNN50 among students in meritocratic system compared to the traditional one. However, this trend reached the level of statistical significance in the students of SG-1 compared to the control (SG-3). In meritocratic education different student groups differed in the level of school stress in 6th and 7th grades. Students in SG-1, compared to SG-2, characterized by lower values % HF, HFn, pNN50 against the background of higher values of % LF, LFn, LF/HF, IC, CC1, CC0. Thus, a higher level of school-based stress in conditions of meritocratic education is determined not so much by the intensification of the educational process as by social factors of the educational environment and/or individual typological traits of students.