The importance of non-governmental organizations (NGOs) in any sector of the economy cannot be under-emphasized. This is because NGOs support services for free that would otherwise have to be paid for. This study aims to examine how NGOs can remain afloat in their performances while using budgetary control techniques. Three selected NGOs in the health sector were Family Health International, Achieving Health Nigeria Initiative, and Management for Science and Health. The independent variable was budgetary control and comprised budgetary planning control, monitoring, and evaluation, while the dependent variable was profit after tax. The study used primary data and 150 questionnaires, allotted and distributed to the staff of the three selected non-governmental organizations: Family Health International 360, Association for Reproductive and Family Health, and Management for Science and Health. The 134 questionnaires were retrieved and analyzed using the ANOVA regression. The findings showed that budgetary planning and budgetary monitoring significantly influence and enhance the performance of NGOs in Nigeria, and budgetary evaluation impacts their performance. This study recommended that the budget department in any non-governmental organization should organize seminars on budgetary controls for its employees to show them the importance of budgetary control and achieving stated objectives with the budget.