The station was built on the Ferrocarril Panamericano, a line that, since 1908, connected the towns on the coast of Chiapas and Soconusco.

The line also connects the Ferrocarril Transístmico with Guatemala.

On 1 November 1904, the 192-kilometer stretch from San Jerónimo to Polka, passing through Juchitán, was inaugurated.

However, the 8.2 magnitude earthquake on 7 September 2017 caused damage.

The building was recovered with the participation of the Alfredo Harp Helú Foundation and a year later, the Juchitán city council decided to rename the station in honor of José F. Gómez, as it is currently known.