Compliance has become one important thing in implementing health protocol during the covid-19 pandemic period. It is the key of success for some schools or education institutions in applying the regulation of limited face-to-face learning (PTMT) during the pandemic. PTMT regulation has been implemented to support the teaching and learning process when the students were at schools. In the implementation of the program, there were some schools, Junior High School (SLTP) and Senior High School (SLTA), both public and private, where the students did not obey the health protocol regulation and there were incomplete supporting facilities available at the schools. This research aims at finding out the differences between health protocol implementation compliance in SLTP and SLTA during PTMT. Methods: The design of the research was comparative descriptive utilizing quantitative technique. The sampling applied stratified random sampling technique. The total respondents were 100 students where 25 students were taken from each school. The data collection used observation, demographic data, and implementation of health protocol compliance questionnaire. The data analysis applied Mann-Whitney’s test. The differences in compliance level shows p-value score of 0.512 > 0.05 indicating that the compliance levels in SLTP students, both public and private, are not different. The p-value score of 0.274 > 0.05 means that there is no different compliance level in SLTA students, both public and private. The p-value score of 0.464 > 0.05 indicates that there is no different compliance level in SLTP and SLTA students. There is no different compliance level in public and private SLTP students during PTMT, there is no different compliance level in public and private SLTA students during PTMT, and there is no different compliance level in SLTP and SLTA students during PTMT.