The authors on the basis of domestic and foreign experience of regional programming analysis justify the need to expand the scope of the federal target programs in the regional management, analyze the reasons underlying their decreased efficiency and popularity. The situation in the field of study is thoroughly analyzed with emphasis on poorly studied aspects of programming, such as: rationale and selection of progressive forms and methods of development and implementation of federal targeted programs taking into account peculiarities of the current situation in Russia and its regions, the role of the federal targeted programs as a regional management tool and the use of financial resources. The article focuses on the use of federal targeted programs as a method of the Altai Territory economy and social sphere management. This section of the article reveals the general pattern of federal targeted programs funding for over a decade, as well as a number of specific aspects of their implementation. The key federal programs are highlighted, the part of funding allocated to each program, the role of the territory in co-financing the programs are described. The systemization of topical challenges and prospects of the target programming development (search for additional sources of financing, implementation of the programs in case of changes in their duration and subordination, the description of the main ways of improvement and methodological approaches to the development and implementation of federal targeted programs, etc.) made by the authors on the basis of academic literature analysis is of particular interest. The authors proposed ways of improving the development and implementation of federal targeted programs covering both problems in methodology and methods of forming the federal program and the problems of organizational and resource constraints.