A. S. Makarenko as a scholar, theoretician, novator, experimentátor and prognosticator of education in the socialist society has contributed creatively also to the methodology of scientific thinking in education. This article points to two main aspects of Makarenko’s contribution. The first one concerns Makarenko’s conception of pedagogical logics that is narrowly related to the general methodology of the science of education. Makarenko thought the key question to be recognized in the relations between the aim and means. The term pedagogical logics was understood by him as the application of the materialistic dialectics in the area of creative pedagogical thinking and practical skill in education. In connection with it the author of this article points to the problematics of the unity of dialectics, logics and theory of knowledge and shows how Soviet authors have solved the problem. Another significant aspect is the fact that A. S. Makarenko, for the first time, realized and applied a systematic approach as a methodological principle of the materialistic dialectics to the practice within his educational activity — since no means could be correctly understood when isolated from the whole system. In this connection the author has shown what sort of views A. S. Makarenko had expressed in the period of the beginning of socialist education.