The tunnel was originally proposed by the Canadian Northern Railway (CNoR) to provide access to Downtown Montreal without having to cross the already-congested area south of Mount Royal or the route around it to the east.

The structure gauge of the Mount Royal Tunnel limits the height of bilevel cars to 14 feet 6 inches (4.42 m).

Exo also considered rerouting its Saint-Jérôme line to Central Station via the tunnel from its current termini at Parc or Lucien L'Allier to save 15 minutes.

The tunnel was conceived in 1910 by the Canadian Northern Railway (CNoR) as a means to give the company access to downtown Montreal.

Likewise CNoR preferred a direct route as opposed to detouring the railway around the north and east sides of Mount Royal.

CNoR also planned a downtown terminal and associated office and retail developments for low-priced lands at de la Gauchetière Street and McGill College Avenue.

On December 10, 1913, crews from the east and west portals met beneath Mount Royal; they were out of alignment by 1 inch (2.5 cm).

Lining of the tunnel bore with concrete was completed by 1916 and the 2 parallel standard gauge tracks and 2400 V DC catenary were installed by September 1918.

At the same time, the newly appointed board at CNoR was directed to take over the operation of the government-owned Canadian Government Railways (CGR).

In the late 1950s, the remainder of the CNoR lands acquired in downtown Montreal during the Mount Royal Tunnel project were developed by CNR.

On June 2, 1995, the last of the GE boxcab electric-powered locomotives delivered to CNoR in 1916–1917 for use in the tunnel were retired by CN after nearly 77 years of service.

Trains were operated with dual-powered ALP-45DP locomotives, and initially ran under electric power to the Ahuntsic station, where they changed over to diesel.

The new platforms will allow direct connection to the Metro from the REM, though in the case of Édouard-Montpetit this will involve a long trip by elevator; it will become Canada's deepest transit station at a depth of 75 m (246 ft 1 in).