The tracks are state-owned and administered by the Swedish Transport Administration, while the operation of the Stockholm commuter rail services itself has been contracted to SJ AB since March 2024.

New trains were bought, stations were modernised, and the Stockholm commuter rail network was developed with an aim of making it more metro-like.

Trains on the Kungsängen branch now terminated at Västerhaninge instead of Stockholm C and which now forms part of the modern line 35.

A southern infill station at Årstaberg was inaugurated in 2006, in order to connect with the then new Tvärbanan tram system.

The implementation required negotiations between Stockholm Transport and Arlanda Express, who had operating rights for the tracks.

This eases the rail systems' congestion problems, and permits Stockholm Transport to schedule more frequent service.

The first franchise holder was Citypendeln [sv], which operated the Stockholm commuter rail from 2000 until 17 June 2006.

From 18 June 2006 until 10 December 2016, the network was operated by Stockholmståg [sv], a subsidiary of SJ AB, the former Swedish State Railways company.

[8] In May 2023, SL decided not to extend MTR Nordic's contract to operate the Stockholm commuter rail beyond 2026, citing service delivery issues.

[9][10] On 1 November 2023, SL awarded an emergency contract to SJ AB, which took over operations from March 2024.

Line 40, 48 and the outer parts of the railway to Nynäshamn (from Västerhaninge) are served less frequently, with up to one hour between trains on weekends.

Most stations are of a similar style, with an island platform in a ground-level location with one or two exits, turnstiles, and a staffed ticket office.