Most of existing researches on the methods of governance in the European Union (EU) are rather narrow in scope. Many of them investigate particular policies of the EU for the purpose of identifying and describing the details of the governance mode in use. Other researches provide a comparative analysis of the application of a particular method of governance in several EU policies. However, there is a clear lacuna in the field of systematization of all methods of governance usable in the EU. This article reveals a comprehensive system of EU methods of governance. They are based on six key principles: 1) EU methods of governance are not reducible to combinations of communitarian and intergovernmental approaches. 2) Methods of governance are linked with the level of decision-making (super-system, system and subsystem decisions). 3) There are seven basic methods of governance in the EU. Classic intergovernmental method is used to make “historic” decisions at the super-system level. Communitarian approach and intensive trans-governmentalism are the most common methods at the system level. One can distinguish four methods of governance at the subsystem level: regulation, distribution, policy coordination and executive method. 4) There is no univocal correspondence between methods of policy setting (system level) and policy implementation (subsystem level). 5) Identified methods of governance are the ideal types. In practice, implementation of particular policy in the EU is usually a combination of various governance methods. 6) Methods of governance used at the level of policy implementation could change in the course of time. The concept proposed reflects the inter-coupling between the level of decision-making and a method of governance in the EU. It offers a consistent systematization of EU methods of governance, and discloses the correspondence between methods of governance and EU policies. Developed theoretical concept can be used as a methodological basis for the research of EU activities in particular policy areas, of decision-making process in the EU, of the evolution of governance in particular policy areas.