Construction began in the late 19th century with the first segment from Wadi Halfa to Abu Hamad and has grown substantially in the century that followed. In 1906 a major milestone was achieved as Khartoum linked with the new seaport of Port Sudan. It provided direct connections to ocean-going transport, forming the core of the present-day network.

A line was built from Khartoum southward to Sennar, the heart of the cotton-growing region of Al Jazirah. In 1911 a westward continuation reached El-Obeid, then the country's second-largest city and the center of gum arabic production. Over the first decades of the 20th century, the line expanded from near Abu Hamad to Kuraymah in Northern Sudan, reaching 5,808kms.

Sudan Railways played a strategic role during the First World War. Afterward, the country entered a period of peace and stability, and the government looked to tie other parts of Sudan to the capital. In the 1920s, the main line extended from Hayya south to a junction with the mainline at Sennar.

With a growing emphasis on export and passenger transport, there was a further push to expand links across the country in the mid twentieth century and the railroad added capacity and new facilities in Khartoum. The Gezira project, one of the world's largest agriculture schemes, relied on over 5000km of new track to ensure its main exports, cotton, and wheat, could be transported efficiently to markets.

Following independence in 1956, the new Sudanese government viewed the railroad as a critical way to develop and bring prosperity to the country. Further extensions continued through the first half of the 20th century, culminating with 4700km of track. In 1959 the final construction phase extended the western line to Nyala in Darfur. In 1961 a southwesterly branch to Wau, southern Sudan's second-largest city, essentially completed the network.

In 1995 there were extensions from Abu Gabra to El Muglad (52km), El Obeid to the refinery (10km), and El Ban to the Merowe Dam (10km). During the 1970s and 1980s, Sudan Railways was a best-in-class operator, connecting mines in the west to cotton and wheat fields in the east and onto the Red Sea.

The Sudan Railways Authority is receiving 21 new locomotives from the Chinese company CRRC Ziyang, which departed from the Chinese port in mid-June 2022 and is expected to arrive in Port Sudan in the first week of August. Out of the 34 locomotives agreed on in a contract signed between the Sudan Railways Authority and CRRC Ziyang in September 2020, these 21 new locomotives would be the first batch received. As an important achievement of the authority, this project has received great attention from the governments of Sudan and China. With the arrival of new locomotives, the rail transport capacity is expected to significantly improve, becoming a great contributor to raising the country's economy.