General phenomenon in Indonesian states that universities in this country are still haven’t implement the principles of Good University Governance. Universities have strategic role in advancing science and technology by applying the value of the humanities as well as the cultivation and sustainable empowerment of the nation in accordance with Law No. 12 Year 2012. This study uses a technical judgment sampling survey with Research and development approach. The results of research outcomes in form of web based budget implementation called Management and Financial Accounting Information System in Higher Education (SIMAKU-PT) with features: Performance based Budgeting, financial administration, accounting in accordance with Statement of Financial Accounting Standards (PSAK) No. 45 of not for profit accounting with integrated accrual basis. SIMAKU-PT is able to produce a performance-based budget based on strategic plans of Higher Education according to the principles of money follow function and value for money, it is able to support the system of disbursement and accountability of funds in a transparent and accountable use of the money should accounted mechanism with a system of imprest fund or fixed funds, and able to produce financial reporting integrated with the budget include are: budget realization reports, activity reports, statements of financial position and cash flows in accordance with the provisions of PSAK No. 45. The model supports financial governance for College transparency and accountability towards Good University Governance. This study was the first in Indonesia which produce innovative technology in universities governance. Research products have been implemented in some universities such as University of Muhammadiyah (UM) Yogyakarta, UM Jember, UM Tangerang and School of Transport Management (STMT) Trisakti.