The partition of India in 1947 completely disrupted communication links in North Bengal and Assam with the southern parts of West Bengal. Earlier, the links were through the eastern part of Bengal, which became a part of Pakistan in 1947. Siliguri gained in importance as the gateway to North Bengal, Sikkim, Bhutan and Assam.
Around 1949, Siliguri Junction station, a new station north of the old Siliguri Town railway station, came up with several metre gauge lines converging on it. In addition there was the narrow gauge Darjeeling Himalayan Railway running from Siliguri Town station to Darjeeling via Siliguri Junction. The Assam Rail Link Project, completed in 1950, linked the railways in Assam, with a metre gauge line to Kishanganj. The line running across North Bengal, spanned the Teesta, Torsha, and Sankosh rivers.
In the early 1960s, Indian Railways started changing over from metre gauge to broad gauge and built a new 1,676 mm (5 ft 6 in) broad gauge station south of Siliguri Town station. It was intended to name the station New Siliguri station. However, as the new station was located in Jalpaiguri district, it was named New Jalpaiguri station. By 1964, New Jalpaiguri became the most important railway station in the area. It had both broad gauge (to Kishanganj and Barsoi) and metre gauge (to Siliguri town and Siliguri junction) tracks. The Darjeeling Himalayan Railway narrow gauge track was extended from Siliguri town station to the new greenfield station. The metre gauge track from New Jaipaiguri to Siliguri town and Siliguri junction was later converted to broad gauge.
New Jalpaiguri railway station has two double-bedded air-conditioned (AC) retiring rooms, six double-bedded non-AC retring rooms, one three-bedded dormitory and one twelve-bedded dormitory. Other amenities include computerized reservation counters, vegetarian and non-vegetarian refreshment rooms and book stall.
New Jalpaiguri railway station is amongst the top hundred booking stations of Indian Railway.
More than a hundred trains pass through New Jalpaiguri station. Seven express trains and six passenger trains originate and terminate there as of August 2012.
New Jalpaiguri handles the Guwahati Rajdhani Express, Brahmaputra Mail, Darjeeling Mail and Howrah - New Jalpaiguri Shatabdi Express trains. Trains with longest east-west run in India include 15905/15906 - Dibrugarh Town to Kanyakumari Vivek Express. This weekly train; numbered 15905/15906, is currently the longest train route in the Indian subcontinent. It travels a distance of 4286 km in 82:30 hours (almost 4 days), Guwahati-Trivandrum Express covering 3,474 km, Guwahati-Okha Express covering 3,222 km, and Guwahati-Dadar Express covering 2,657 km. All these trains pass through New Jalpaiguri railway station.