The Northeast Frontier (NF) Railway has its historical roots in the former Assam Railways & Trading Company, Assam Bengal Railways, and Eastern Bengal Railways. The Assam Bengal Railways had the largest contribution to make in the formation of the present-day N. F. Railway.

Assam Railway P. Trading Company laid the first Railway line in Assam upto Makum collieries at Margherita in 1884. The Company also established the first passenger Railway system in Assam under the name Dibru Sadiya Railway. The Eastern Bengal Railway constructed the sections Haldibari - Siliguri, Barsoi - Kishanganj, Manihari Katihar- Kasaba and opened these sometime before 1900. They expanded the network to other sections namely, Hasimara - Alipurduar, Gitaldaha Bamanhat, Golakganj - Amingaon, Rangiya - Rangapara & Dhubri during the period 1900-1911. The Assam Railway & Trading Company, the Eastern Bengal Railway and the Assam Bengal Railway which was also operating in the Barak Valley region, were merged during World War II and came to be known as the Bengal Assam Railway. Thereafter, some of the Company-owned Railways namely, Bengal Dooars Railway, Jorhaut Provincial Railway, Chaparmukh Silghat Railway and Katakhal Lalabazar Railway etc. were merged with the Bengal Assam Railway system.

With the partition of India in August 1947, the Bengal Assam Railway was bifurcated according to the political boundaries, leading to the formation of the Assam Railway with its headquarters at Pandu. In 1948 the Darjeeling - Himalayan Railway was also taken over by the Government of India and merged with Assam Railways.

The partition of the country and formation of the erstwhile East Pakistan (now Bangladesh) led to complete severance of communication with the State of Assam from the rest of India. It was restored with the completion of the Assam Rail Link Project in January 1950.

During the reorganisation of Railway zones in 1953, Assam Railway and Avadh - Tirhut Railway were merged to form the North Eastern Railway with headquarters at Gorakhpur. The N. F. Railway system was carved out of the North Eastern Railway on 15th January, 1958 and based at Maligaon, Guwahati at the foothill of Nilachal 'Parbat', the abode of Goddess Kamakhya.

N. F. Railway is the smallest of the 9 zones on the Indian Railways, but has the unique distinction of serving as many as ten States of the Indian Union, namely Arunachal Pradesh, Assam, Bihar, Manipur, Meghalaya, Mizoram. Nagaland, Sikkim, Tripura and West Bengal. Besides, it also serves as a rail-head for the Himalayan kingdoms of Nepal and Bhutan and provides interchange facilities with Bangladesh Railway.