The Pier Railway crossed over the Mallaig Extension Railway of the London and North Eastern Railway to the north of Fort William Junction, which was known as Mallaig Junction at the time, crossed the A82 road at a level crossing, and then crossed the West Highland Railway.
The pier railway, built to enable construction materials to be brought in, ran  from a pier on Loch Linnhe to "Base Camp", to the north and north-west of the factory site.