They were completed in 1854, 1855, and 1902 by the Pennsylvania Railroad as part of the cross-state route that includes the nearby Horseshoe Curve to the east.

Their ownership has since passed to Penn Central Transportation Company, then to Conrail, and most recently to the Norfolk Southern Railway.

In the early 1990s, Conrail (with money from the Commonwealth of Pennsylvania) enlarged the Allegheny and New Portage Tunnels to accommodate double-stack container on flatcar (COFC) trains.

The Allegheny Tunnel was enlarged from its original 1854 cross-section to contain two tracks that could be used for double-stack rail transport in either direction.

The museum, which sits across the street, has exhibits about the area's railroad, industrial, social, and religious heritage; a gift shop, and a theater.