Prior to the formation of Assam Christian Council (ACC) in 1937, churches in Assam region were under the umbrella of Bengal Christian Council (BCC). However, as issues and problems in Assam region were different from those in Bengal, it did not take long for leaders in the region realize the futility of staying in that Council. The American Baptists was the first to withdraw, while the Welsh Presbyterian continued to stay on 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 attended a follow-up meeting held in April 15, 1937 from various Churches and Missions in the region. 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 2019, it has 52 constituent units, that include 35 churches and 17 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 two ongoing projects: Union Christian College and Union Christian College Higher Secondary School at Umiam Khwan (Barapani), Meghalaya.