The SARCC owned commuter rail-related assets, including stations and surrounding land, infrastructure and rolling stock, while the services were operated by Metrorail.

On 1 December 2004, the South African Cabinet decided to integrate the current state-run passenger rail and bus services under one organisation which at that time was managed by the SARCC and Transnet, so as to improve the accessibility, safety and cost to the consumer.

Between 2011 and 2021 PRASA experienced a significant fall in its ability to fulfill its mandate to provide rail based public transportation in South Africa's urban areas.

[4] High levels of corruption, maladministration and mismanagement, largely associated with the presidency of Jacob Zuma, were blamed for the fall in the state owned enterprise's ability to provide basic rail passenger transport services.

The Afro 4000 requires 4.14 meters of clearance, too high for SA rail infrastructure at 3.965 m.[7] Resulting scandal led to the 2015 removal of CEO, Lucky Montana and his chief engineer "Dr." Daniel Mtimkulu.

[9][10] In mid-August 2019, Transport Minister Fikile Mbalula launched a war room with a 100 day plan to improve PRASA's railway network and to plot its progress.

[11] Early December 2019 saw Transport Minister Fikile Mbalula fire the PRASA board and its chief executive officer and placed the organisation under administration after failing government audits and their inability to stabilise its financial position and market share.

[12] Administrator Mpondo announced in January 2020 that he had closed down the war room created by the minister five months earlier, and he formed five exco subcommittees called revenue enhancement and cost containment; governance; service recovery; safety management; and capital and modernisation programme acceleration.

[13] In February 2020, Eskom cut power to PRASA's Western Cape rail network after they failed to pay R4 million overdue electricity account but was restored after payment.

[15] Also in February 2020, Tembinkosi Bonakele of the Competition Commission made recommendations for the unbundling of certain divisions of PRASA after an investigation into the public transport market in South Africa.

[16] By 2022 Minister Mbalula announced that PRASA was no longer able to secure its trains and infrastructure as criminal syndicates had managed to infiltrate the company to facilitate wide scale metal theft.