In this paper we present methods, data and algorithms for simulating budget system in the model of the Russian Federation spatial development. We show the place of this task in methodology of our research and give a brief overview of the background results. Key objects of the budget system in the model are the federal budget, regional budgets and extra budgetary funds: pension, medical and social insurance. We determine revenues and expenditures of the budgets and funds on the basis of federal laws, Budget and Tax codes of the Russian Federation. Since the exact reproduction of excise rates and customs duties is problematic due to model aggregation, we calculate model rates of excises and duties for selected sectors on the basis of retrospective data pre sented on the budget system portal and in the federal input-output table. Structure of the budget expenses in the model was simplified by aggregating expenditure items into major groups correlated with sectors of the economy. Presented algorithm of the budget system simulates interaction of the federal, regional budgets and extra-budgetary funds with agents and organizations in the model. For validation of the budget system algorithms in the model we conduct retrospective modeling for the federal budget and the budget of Belgorod region in 2014.