Waqf is a charitable institution within Islam and Muslim contexts. Waqf translates to an endowment held in trust and is utilised for charitable purposes such as education, poverty alleviation, a place of worship, or medical care. In the educational development, waqf has funded many Islamic educational institutions, colleges, universities, libraries, and the like. In the context of Indonesian society, the modern system of waqf institution has been implemented to establish the pesantren (Islamic schools) and Islamic universities. This paper presents the example of waqf in education that has been practised in Indonesia. Darussalam Gontor is taken as an example since it is well-known as the first modern pesantren in Indonesia, endowed in 1958. It is a successful waqf-based educational institution. In reality, waqf-based institution can generate significant benefits in support of education and community development. The study shows the values-based management at the core of this waqf-funded Institution and reveals the concept of waqf basyr (Human waqf) which looks at the contribution of human resources. In addition to this essay also highlights the internal control practiced preserving the pesantren’s operational sustainability and to mitigate the mismanagement. This study is based on recent qualitative research comprising both primary and secondary data. The primary data included interviews with the core and peripheral respondents within the Institution. Secondary data was collected from in-depth literature reviews including the annual report of this Institution, books, journal articles, and relevant data and documents. The study's finding presents how the values-based education and human waqf implemented in this pesantren could be a role model for supporting the educational development system in the modern world. Additionally, the result of study shows that the internal control can mitigate the miss-managements and enhances the sustainability of the operational of this Institution. Importantly, there is a need to broadly bring values-based management, skilled human waqf (as human resources), and internal control to the educational or waqf institutions to enhance their operational sustainability and support their impacts on community development.