Construction of Nynäsbanan was started by the private company Stockholm-Nynäs Järnvägs AB in 1898 and the line was opened on 28 December 1901.

Nynäsbanan was nationalised in 1957, although Stockholm-Nynäs Järnvägs AB continued to exist at least on paper until it was fully absorbed into the Swedish State Railways in 1968.

The line was electrified in 1962, and in 1973 it became part of the Stockholm Commuter Rail, when at the same time X1 electric multiple units were introduced.

A modern Automatic train control (ATC) signalling system was introduced on Nynäsbanan in 1980.

[6] In connection with the expansion of the Stockholm Norvik freight port, a siding was built from the Nynäs line towards the harbour, which was completed in April 2020.