Article (7) of the National Spatial Planning Document emphasizes the development of regional development programs, five-year economic, socio-cultural development plans, and the formulation of annual budgets in line with achieving spatial planning objectives. However, the fiscal year 2023–2024 budget, as the first budget after the approval of the spatial planning document, was not aligned with this program. The link between planning and budgeting is achieved within budgeting systems that have a longer-term horizon. The Medium-Term Expenditure Framework (MTEF) is a model for defining an institutional mechanism for preparing and approving budgets over the medium term. This paper, for the first time, employs the MTEF with the aim of establishing a meaningful connection between the budgeting system and national policymaking and planning. It designs a Spatial Planning-Based Budgeting (SPBB) process as a multi-year budgeting system and proposes a new mechanism for resource allocation based on regional and spatial development priorities at the national level. Additionally, as a case study, based on the East Azerbaijan Province spatial planning document and the prioritization of its national and provincial development projects in 2023–2024, it examines the implementation of this model for the transportation sector of the province. The results indicate that in spatial planning-based budgeting, annual budgets serve as executive tools for long-term plans, whereby budget allocation is based on development priorities and in line with achieving the overarching policies of spatial planning.