Three years after Asom (Assam) had come under the control of the British, the Baptist Missionary Society(B.M.S) or the English Baptists through the Serampore Mission, opened a school at Guwahati in 1826. Soon after, schools were opened at Cherrapunji, Mawsmai and Mawmluh, marking the beginning of Khasi literature. In 1836, two American Missionary couples came to Sadiya, and soon moved to the hills. Missionaries from different nations and of different denominations started schools and later colleges across the North East.
In 1940 a Christian University was apparently proposed to be started from Jorhat but it did not materialize. In 2010, PRINCIPALS OF THEOLOGICAL SEMINARIES UNDER CBCNEI unanimously voiced their hope to establish full fledged university. Their dream was the North East Christian University, This was followed by –
- Series of consultations within Baptist Convention and Association leaders under CBCNEI to establish NECU as a reality.
- The NECU act adopted by the Nagaland Legislative Assembly.
- An area within dimapur city acquired through the Nagaland Baptist Church Council (NBCC) to establish the NECU city centre.
- 250 acres for the NECU campus made available for the university by the Government of Nagaland at Medziphema Village.