Bowdoin was closed for two periods in the early 1980s due to budget cuts; it was open for limited hours on weekdays only until 2014, when it returned to full-time service during the reconstruction of nearby Government Center station.

[1] Court Street proved to be a problematic terminus; its stub-end single-track design limited frequent service and resulted in several fatal crashes.

[11] Bowdoin was built with a wedge-shaped island platform inside a balloon loop, which eliminated the awkward end-changing required at Court Street and allowed use of unpowered trailer cars in the tunnel to increase capacity.

[12] The station had two staircase entrances at the west end of Bowdoin Square, adjacent to the Parkman building.

[16][12] Though originally planned to use high-floor rapid transit trains, the East Boston Tunnel opened with streetcars serving low-platform stations.

[17]: 19  Large bi-loading streetcars (with high floors but capable of loading from low platforms), which incorporated many attributes from metro cars used on the Main Line El, began use in 1905.

[17]: 118–119 [18]: 14  However, neither these nor the large center-entrance cars introduced in 1917 (which were designed for multiple unit operation) could fully handle the crowds.

[19] The next year, the BTD board approved the construction of high-level platforms at Atlantic Avenue, Devonshire, Scollay Under, and Bowdoin.

[9]: 32  When the first phase of the Revere Extension opened to Orient Heights with a new maintenance facility in 1952, the connection was no longer necessary and the portal was filled.

[4][3]: 65  The new headhouse, near the middle of the station, was designed by Josep Lluís Sert as part of a project for a never-built Catholic chapel nearby.

MBTA Commuter Rail service to Providence and Concord and on the Woburn Branch was cut entirely, five underused commuter rail stations were closed, Boylston and Essex were closed for short periods, and the outer ends of the Orange and Blue lines were bustituted on Sundays.

[30][1] It reopened on January 11, 1982, but only on weekdays until 6:30 pm – intended to serve workers in nearby office and government buildings.

The closure would take place after the renovation of Government Center, which would re-add a long-closed entrance at the west end of the Blue Line platform.

[33] Because the eastbound side of the Bowdoin platform can only fit four cars, the MBTA had originally planned to close the station when six-car trains entered service; a planned renovation of Government Center station was to add a second headhouse close to Bowdoin Square.

[35] However, by 2013, the MBTA decided not to construct the planned west entrance at Government Center, and to instead build only a less-expensive emergency exit.

[1] In February 2016, the MBTA announced that Bowdoin would remain open at all times even after Government Center reopened on March 21.

[40] In 2019, the MBTA indicated that Bowdoin was a "Tier II" accessibility priority pending the results of conceptual design.

[5] A 2018 update which analyzed multiple tunneling methods only considered an extension without a replacement Bowdoin station, as did a 2020 conceptual design.