An urgent problem of modern science is the formation of a scientific methodology for managing logistical provision for the development of innovative cooperation in circular economy, since the desire of scientists to add their own contribution to science is explained by the desire to develop and improve it in order to expand the range of both theoretical and practical issues that can be solved with the use of modern terminology. The article is aimed at forming methodological principles for managing logistical provision for the development of innovative cooperation in a circular economy. The research of formation of the essence of methodology is carried out, the stages of development of methods and means of scientific knowledge are analyzed. The definition of «methodology» is systematized and analyzed, which allows to determine the basics of formation of methodological principles for the management of logistical provision for the development of innovative cooperation in the conditions of circular economy, namely: approaches, principles, categories, functions, instrumentarium, paradigm. The categorical, conceptual and instrumental-model levels of the methodology for managing logistical provision for the development of innovative cooperation in the conditions of circular economy have been distinguished and characterized. The connection between the empirical and the theoretical methods of scientific cognition is considered and defined. It is proved that as a conceptual module of the methodology for managing logistical support for the development of innovative cooperation in a circular economy should be considered a metatheoretic unity based on the ontological and gnoseological idealizations – the methodological paradigm.