Economic instability, continuous change of conditions, that innovatively oriented enterprises function in, complicate the achievement of planned results and decrease the efficiency of using strategic management of the development. Taking into account the aforesaid, the aim of the article is to elaborate a conception of providing the operational development in the functioning process of innovatively oriented enterprises, based on the complex of operational actions (economic functions), achieving tactic and strategic purpose-oriented results for transferring the economic system of an enterprise in the new development stage. According to research results, it was grounded, that the aim of functioning of innovatively oriented enterprises at realizing the operational development process forms as a combination of the innovatively oriented evolution of the economic system and the increase of the economic return for the further use in the development process. It was proved, that the development at the operational level is a process of purpose-oriented changes that provide transferring an enterprise to the new development stage. Such purpose-oriented changes are offered to be realized through realizing economic functions in the internal environment of an enterprise, directed not only on current functioning processes, but also development that allows to attain the sufficient economic return level. It was revealed, that it is expedient to realize them, based on using factors of production and management of economic relations both at the level "subject-object" and "object-object", considering an innovatively oriented enterprise as an ecosystem. For this aim, its construction and structure are grounded; the characteristic of key complicated functional environments of components of an ecosystem is given. It was elucidated, that the economic evolution of an enterprise takes place through the change of stages (phases) of the functional development level, at each of them the complex of economic functions is realized, and the economic return is obtained according to an achieved position in the development process.