Sweden's first railway tunnel was constructed in Nyboda as part of the extension of the Western Main Line to Stockholm in 1860. Excavation work began in July 1858, breakthrough occurred in September 1859, and the 276-metre-long tunnel was completed in June 1860. The work was carried out by prisoners from Långholmen Prison, manually using black powder and hand-operated cranes, under the supervision of guards armed with rifles.

It was a very large and costly infrastructure project for its time. In the book about the Sammanbindningsbanan (Interconnecting Railway Line) from 1870, the construction works from the south are described as follows:

"On the last stretch of the Western Main Line, as it approaches and enters Sweden's capital, the largest and most characteristic works of Swedish railway construction occur. Few railways, both inside and outside the country, probably offer a similar succession of individually remarkable construction works over such a short distance. As one approaches Stockholm from the south on the railway, one encounters the Nyboda Tunnel, blasted through a particularly hard gneiss rock. The Nyboda Tunnel has a length of 935 feet, is 18 feet high and 18 feet wide, with a depth from the highest peak of the rock to the tunnel's vault of about 100 feet, and the cost of the work amounted to around 150,000 Riksdalers."

Another tunnel was added in 1909 as part of the construction of a double track to Stockholm, which is now used as an industrial track.

When the Årsta Bridge and Liljeholm Bridge were inaugurated in the late 1920s, railway traffic to Stockholm was redirected onto a new track section. An industrial track ran through the original Nyboda Tunnel, which was decommissioned in 1967 when the Essingeleden motorway was built. The rails have since been removed, and the tunnel openings sealed.