The first railway to open a station in Barra Funda was the Estrada de Ferro Sorocabana, on 10 July 1875.

On 19 May 1892, São Paulo Railway opened their station, a few meter ahead, after Viaduto Pacaembu.

The current station was built by the São Paulo Metro with resources from the State and Federal Governments, in the location of the old Estrada de Ferro Sorocabana station, to attend the East-West Line (current Line 3-Red) and unify in only one station the FEPASA and CBTU commuter trains.

During the construction, in May 1986, a favela was displaced, which was located onder the adjacent Viaduto Antártica, paying Cz$ 6,000 for each family.

[2] On 27 April 2006, the Metro station was renamed to Palmeiras-Barra Funda, a tribute to Sociedade Esportiva Palmeiras, a São Paulo soccer club headquartered 750 metres (2,460 ft) away from the terminal.