The article describes the experience of developing and testing methods for large-scale application of the method of individual educational trajectory in the bachelor's degree. The research methodology, which includes a synergetic approach, the theory of self-organization and the principles of nonlinear dynamics, allowed: to form a generalized definition of the concept "method of individual educational trajectory"; to determine the stages of development of a person's ability to build their own learning trajectory; to identify the specifics of using this method at the stage of professional education; develop and test experimentally the goals, content, methods of control, evaluation, conditions, forms, means, and projected results of the method. the article presents the results of experimental verification of the method of application of the method. The experiment was conducted at the southern Federal University in 2016-2008. its participants were two teachers and 100 students of the 1st-4th year (future teachers of biology and chemistry) of the pedagogical direction of the bachelor's degree.