Pakenham is an elevated premium station, featuring an island platform with two faces.

[4] Like the suburb itself, the station is named after Sir Edward Michael Pakenham, a major general who served in the Peninsular War.

[5] In 1938, flashing light signals were provided at the former Main Street level crossing, which was located at the up end of the station.

[9] On 16 April 1980, Pakenham was the scene of a collision between Hitachi carriage 353D and guards van 286ZL.

Works will continue on the northern side for the construction of permanent stairs and lift until late 2024.

Ventura Bus Lines operates six routes via Pakenham station, under contract to Public Transport Victoria: Warragul Bus Lines operates one route to and from Pakenham station, under contract to Public Transport Victoria: Westernport Roadlines operates one bus route to and from Pakenham station, under contract to Public Transport Victoria: