Synod Office Administration Department: This Department looks after all the matters related to the administration of the Synod Office.

Finance Department: This Department deals with all matters relating to its finance, subject to the approval of the Synod or the Executive Committee.

Pastoral Ministry Department: This Department looks after the intensive and extensive tasks of all the Pastors and Pro Pastor. Besides posting of Pastors to different Pastorates, the Department also deputes Pastors to Special Posts to the Presbyterian Church of India, Khasi Jaintia Presbyterian Assembly, and other special posts of the Synod in and outside the state.

Trust Department: This Department deals with all the matters related to the movable and immovable assets of the Synod.

Theological Education Department: This Department looks after the recruitment of new students for theological studies. It conducts Orientation classes for the final year Students every year, and also Pro. Pastors’ Course of reading and examination.

Mission & Evangelism Department: This Department promotes evangelistic and Mission works within and outside the Synod.
The following are the Mission Fields :
Khadar shnong Mission Centre, Upper Shilliang Khri Mission Centre, Nongjri Mission Centre, Kyrshai Mission Centre, Dhubri and Kokrajhar Mission. The Dhubri and Kokrajhar Mission are outside the state in the Dhubri District of Assam. Its headquarter is in Gauripur. At present there is two Missionary Pastors, 6 Churches, 551 believers, 16 Preaching Stations, 5 Missionary teachers, 10 Mission Workers, 4 Bibleman and Bible Woman, 16 Teachers 15 staffs and 2 Schools.
Christian Education Department: This department deals with matters related to education. There are 2 (two) Colleges – Synod College and Nabon Synod College. 5 (five) schools – KJP Girls’ Higher Secondary School, Shillong, KJP Synod Sepngi Secondary School, Nongstoin, Synod Higher Secondary School, Shillong, Joel Gatphoh Memorial Higher Secondary School, Kynroh and Mawkhar Christian Secondary School fully managed by the Synod. There are other Schools and Colleges established and managed by the Presbyteries, Districts and local Churches which are being allotted yearly and monthly token grants from the Synod. Besides the syllabi prescribed by the Government the department also prescribes books for moral instructions.
Synod College

Social & Economic Life Development Department: This Department deals with the social works and social issues concerning society. Agency for Sustainable Development Initiatives is a registered Non Governmental Organisation of this Department. It is a non-profit, secular, registered, social and charitable Society under the Certificate of Registration of Societies Act XXI of 1860 under the Government of Meghalaya, Shillong, with a mission to improve the quality of life of the most vulnerable sections of society, particularly those residing in remote rural communities. The programmes of Agency for Sustainable Development Initiatives aim to form partnership with people, communities and resources as to create opportunities which empower, enhance dignity and lead to security of health, food, livelihood and shelter in a sustainable manner.