There is an increased interest in project training in the vocational education system, which allows better and more targeted training of future specialists, and to acquire professionally significant competencies for the organization of project management following the requirements of the employer. A graduate should possess not only fundamental knowledge in the field of study but also many personal qualities, the most demanded of which are: creativity, adaptability, critical thinking, consistency of aim, professional growth ability that formed in the process of project training. Agile technology is widespread in the scientific and educational spheres. This technology recommended itself positively but at the same time the problem of how to integrate the technology in the teaching process of educational organization. There is no univocal way of solving this problem in Russian and foreign literature. The aim of the research is to determine the features of the Agile methodology of project management application in the process of implementing the project method of teaching in student’s training. The Agile methodology used in project management helps to create comfortable conditions for training and research work of university employees and students and provides an opportunity to individualize training. Whereas one to accept the education as a process of the goal achieving one will resolve the problem of the aggregate of the processes management. Due to the new requirements to the roles of the teacher and the lecturer the necessity of revealing the teaching activity through the prism of management technologies and integration the project management approaches and system of the quality management appeared. The main method of the research is informational analytics. The management research methods, such as Benchmarking, Lean Manufacturing, Total Quality Management, and Project Management Body of Knowledge were also used. The implementation of this methodology into training provides to transfer the responsibility for the formation of an individual set of competencies from the teacher to the students partially or fully. The study of educational technologies through the prism of the future employers' requirements will help to avoid a number of managerial mistakes and make the process of applying the project method more efficient. The problem of the Agile implementation that was resolved and approved in other spheres of human activities could be resolved through the description and implementation of Agile methodology in the educational process, that was done in the article. Actually, the algorithm of applying the methodology in educational organizations was described and the possibility of the usage of methods of other sciences in educational processes was denoted. The materials of the article addressed to teachers, methodologists and administrative workers of the vocational education system, additional education who are interested in applying innovations in the organization of the educational process and its rationalization, and individualization of professional training of future specialists. The possibility of the addition of the theory and practice of applying pedagogical technologies in the everyday practice of teaching was revealed.