Gurukul Lutheran Theological College and Research Institute is an Organ of the United Evangelical Lutheran Churches in India (UELCI) and is governed by the Gurukul College Council (GCC), which consists of members from all the constituent churches of UELCI and three ecumenical churches – the Church of South India (CSI), the Church of North India (CNI) and the Marthoma Church.

The Gurukul College Council meets annually to offer directions and to revise policies from time to time for the smooth functioning of the College. The Executive Committee of the Gurukul College Council, appointed by the Gurukul College Council, meets at regular intervals to take decisions that strengthen the day-to-day functioning of Gurukul. The Principal appointed by the Gurukul College Council looks into the academic and administrative matters of the College. The Treasurer appointed by the Gurukul College Council looks into the overall financial management of the College.

The ecumenical nature of Gurukul is reflected in the composition of Governing Board, Staff and Students of the college. Gurukul community composed of staff and students representing UELCI, CSI, CNI, Mar Thoma Syrian Church of Malabar, Orthodox Church, Assembly of God, Mara Evangelical Church, Methodist Church in India, Baptists, Independent and Charismatic Churches.