It is necessary to choose the right methodological and theoretical toolkit for the organization of historical and pedagogical research, which is understood as a set of approaches on which the research is based, as well as the choice of appropriate principles and methods. The methodological concept reflects a set of basic and paradigmatic methodological approaches for substantiating the autonomy of institutions of higher education as a complex pedagogical phenomenon on the example of Ukrainian universities of the 19th and early 20th centuries. Given the complexity, the multifaceted nature of the problems raised in historical and pedagogical scientific works, an important stage of the study is the choice of relevant methodological approaches. The methodological tool helps to create a model of the author’s vision and interpretation of those phenomena, facts and events, defines a view on the logic and stages of the development of a certain historical and pedagogical process, regulates the selection of factual material, represents the axiological parameters, is a kind of axiomatic canon of complex analysis. The theoretical and methodological basis of any research forms the system of scientific approaches; they also define and conceptually harmonize principles and methods, forming a certain epistemological integrity. Real knowledge of one or another phenomenon has a pronounced pluralistic character. As plagiarism of the cognitive process, as A. Maidanov notes, lies, firstly, in the multivariate and polivariations of its numerous components and characteristics, and secondly, in the formation within the subject of the study of a number of search fields. The main reason for the plurality of search fields is the quantitative and qualitative wealth and complexity of most of the phenomena under consideration (especially those with a social nature), the diversity of their species and forms. This is precisely the necessity of applying not one but a system of methodological approaches, while they must necessarily meet the research objectives, as well as the methodological culture adopted by the scientific community and the chosen paradigm for studying historical and pedagogical problems. Despite the phenomenon of autonomy of universities is complex, multifaceted, depends on many factors, helps to effectively organize the activities of the university, has an essential characteristic of academic freedom, the following main methodological approaches are used in the work: systemic, structural, functional, logical, concrete historical, synergetic, anthropological, axiological, civilization.