The tunnel was constructed as part of the Dual Contracts expansion of the subway system, and opened in 1920.

The two new tunnels allowed passengers to make an 18-mile (29 km) trip from Coney Island, through Manhattan on the BMT Broadway Line, to Queens for a five-cent fare.

[9] In late 1960, the New York City Transit Authority voted to allot $300,000 for upgrades to the Montague Street Tunnel's ventilation shafts.

[10] On October 29, 2012, the tunnel suffered severe flooding from Hurricane Sandy and as a result, was closed to train service while repairs were being made.

[17][18] Use of the existing tunnel was considered as an option because the Montague Street Tunnel had surplus capacity, having carried the M train until its reroute from the BMT Nassau Street Line to the IND Sixth Avenue Line in 2010, and the N train during the reconstruction of the Manhattan Bridge from 1986 until 2004.