This paper presents a methodology for comparative assessment of military budgeting systems and practices. It is intended for implementation within the Budget Transparency Initiative (BTI) of the Stability Pact for South Eastern Europe (SEE). The methodology shall allow BTI participants and other beneficiaries to identify promising areas for dissemination of good local practice among SEE countries, as well as areas where all SEE countries lack necessary expertise or experience and the region as a whole would need outside support to improve the military budgeting practices. In a hierarchy of criteria, the methodology covers military budgets, budgeting process, budget execution, and assessment of budget execution. Special attention is paid to the issues of transparency and assurance of integrity of military budgeting. The paper includes a description of an idealised military budgeting process to serve as a benchmark, a comprehensive questionnaire to compare existing systems and practices to the benchmark, sets of possible answers to the questions, and guidance on how to process respective answers to the questionnaire. Potentially, the proposed methodology may be useful in other studies aiming to improve democratic governance, transparency and accountability in the public sector, in particular in the defence and the security sector.