Prior to the formation of the Assam Christian Council (ACC) in 1937, churches in the Assam region were under the umbrella of the Bengal Christian Council (BCC). However, as issues and problems in the Assam region differed from those in Bengal, it did not take long for leaders in the region to realize the futility of staying in that Council. The American Baptists were the first to withdraw, while the Welsh Presbyterians continued to stay with the BBC.
In 1936, the Welsh Presbyterian Mission took the initiative and invited other Missions in the region to an informal meeting/conference to discuss matters of common interests. The meeting was held in Shillong on September 22, 1938. Official representatives from various churches and missions in the region attended a follow-up meeting held on April 15, 1937. Delegates at the meeting unanimously voted for a separate Christian Council for a region. A constitution was drafted and subsequently accepted. The Council called “Assam Christian Council” was formally declared at a meeting held in Shillong on November 23, 1937. In 1962, the name of the Council was changed from ‘Assam Christian Council’ to ‘North East India Christian Council’. It is affiliated to National Council of Churches in India.
In 2024, the Council has 55 constituent units, that include 37 churches and 18 para-church organizations. North East India Christian Council Women Assembly (NEICCWA) and North East India Youth Assembly (NEICCYA) are the two wings of NEICC. The NEICC has three ongoing projects: Union Christian College and Union Christian College Higher Secondary School at Umiam Khwan (Barapani), Meghalaya, and the Peace Centre (Centre for Research, Documentation and Training) with its in office in Shillong.