Users of budget funds and their leaders and managers are legally obliged to implement internal control. The internal control system is a very clearly legally defined area. The main purpose of the internal control system is to ensure the legality and transparency of the spending of budget funds. In addition to ensuring business transparency, the internal control system strives to ensure the management of budget funds in such a way that the funds provide value for money and fulfill the purpose for which they were provided, that access to data and information on the way of spending is available, and that the data is transparent and credible. The system of control over financial accounting operations can be carried out through several forms, such as state audit, internal audit, internal financial control or through budgetary control. The responsibility for the establishment, organization and functioning of the internal control system rests with the leaders. Data on the controls carried out are of public interest and are provided to interested parties. Using the example of a national humanitarian non-profit organization, the paper presents and analyzes the established way of functioning of the internal control system. It also presents the findings of budget supervision and analyzes the report on the performed control as an example of good practice in the conduct of control institutions.