The station is built at the western end of the Cob, the great embankment across the Traeth Mawr, on a peninsula from Ynys Madoc constructed in 1842 to form a slate wharf and a harbour wall.

The buildings continued to be in use as the principal offices of the Festiniog Railway Company and the home of Manager (Mr Robert Evans) including throughout the years of almost total closure from 1 August 1946 to 24 September 1954.

This line runs trains, via the cross town link through Porthmadog, to Beddgelert, Rhyd Ddu, Waunfawr, Dinas and Caernarfon.

With the exception of some early morning and late night movements by works trains, this office is staffed constantly when passenger-carrying services are in operation.

Its remit was expanded in 1997 with the commencement of public services on the Welsh Highland Railway between Caernarfon and Dinas and its subsequent expansion south towards Porthmadog.

Having foreseen this problem, the FR proposed a £1.3M rebuild of Harbour Station, to provide two separate and individually controllable platforms, each with their own run-round loops.