The BPKF is managed by a ten member Board of Directors headed by the two Co-Chairpersons. The Ambassador of India to Nepal and the Nepalese Ambassador to India are the Co-Chairpersons of the Board. Other members of the Board are nominated by the two Governments from amongst the distinguished persons in their respective fields, while the two Joint Secretaries in-charge of their respective Foreign Officers of India and Nepal desks and two officials of respective Embassies are designated to act jointly as Secretaries of the Foundation.

The Board manages, supervises and controls the affairs of the Foundation. It meets twice a year to consider various proposals and projects received by the Foundation, and sanctions funds. Towards meeting the stated objectives, individuals, institutions or groups can approach the Foundation for consideration of their proposals through prescribed format made available in Foundation offices in Delhi and Kathmandu