Background: This study substantiates and defines organizational and methodological conditions to ensure the continuity of the physical education process during the transition from middle to high school. Materials and methods: The purpose of this study was to develop organizational and methodological conditions to ensure the continuity of physical education of schoolchildren during the transition from middle to high school by taking into account the results of pedagogical control of their physical condition. To achieve set goals and objectives and to obtain accurate research results, the following research methods were applied: theoretical analysis, survey, anthropometric and physiological methods, methods for determining the physical performance level, method for estimating somatic health, pedagogical methods of research, and methods of mathematical statistics. Results of the study: On the basis of holistic scientific analysis and to adequately plan educational materials, the main approaches for the differentiation of physical education tools were identified according to the functional capabilities of students during the transition from middle to high school. It was established that after a long period of rest (i.e., summer vacation) there was a decrease in the indicators of the functional state of respiratory system (e.g., vital capacity of lungs and duration of breath-holding on inhalation and exhalation), physical qualities (strength, speed, endurance, speed-strength), and physical performance of schoolchildren. Therefore, it is necessary to improve the content and structure of physical education during the transition from educational (middle school) to the terminative stage of specific orientation (high school). Conclusions: A slowdown in age-related growth was revealed; in some cases, a decrease in absolute values was observed compared to previous measurements after winter and summer holidays.