Two boards of trustees govern Good Shepherd College and Seminary. One based in Africa and another based in United States of America. The Africa based board consists of eleven executive members and six associate members responsible with supervisory roles to oversee the management and operations of the college in South Sudan. This board regularly renders advice on matters related to the functioning of the college while responsible for formulation of policies and execution leadership roles. By articles of incorporation, this board legitimately holds in trust funds, assets, or property belonging to this institution in South Sudan.
In the USA, Good Shepherd College & Seminary, retains its formerly name of the Good Shepherd Leadership Training Center with a non-profit 501 (c)3 status.The USA based board runs GSLTC. The board consists of twelve executive members and two ex-official members. It is responsible for supporting the vision of the college globally with commitment to solicit financial and moral support for the implementation of the college activities in South Sudan and other countries where mobile and short training are offered to clergy, and leaders particulary in the refugee camps in Uganda and Kenya.