The article suggests methodical approaches to the budgeting-based organization of internal control, determines the tasks and subtasks of control that consist in the construction of an efficient system for the making, implementation, control, and analysis of managerial decisions. The organization of responsibility centers by means of implementing budgeting is suggested with a view to ensuring the stable work of independent educational institutions under the conditions of their partial independence. The goal of the development and implementation of a budgeting system is to create an instrument for the efficient organization of the activity management of an institution and its structural units by planning, controlling incomes and expenses, and analyzing economic and financial indicators.