The station previously served Scollay Square before its demolition for the creation of Boston City Hall Plaza.

[5] The Metropolitan Railroad, the largest of the horsecar systems, used the Tremont House hotel a block to the south of Scollay Square as a terminus for many routes.

The three-sided main platform served northbound and southbound through tracks plus the Brattle Loop track, one of two turnback points (along with Adams Square) for streetcars entering the subway from the north; a side platform also served the loop[8]: 23  Boston Elevated Railway (BERy) streetcars from Everett, Medford, and Malden (which formerly ran to Scollay Square on the surface) used Brattle Loop, as did cars from Lynn and Boston Railroad and its successors.

[10] On June 10, 1901, Main Line Elevated trains began using the through tracks through the Tremont Street Subway, while streetcars continued using the Brattle Loop.

[8]: 39  A bronze statue of John Winthrop was relocated from Scollay Square to the Back Bay in 1903 to make room for the exit stairs from the station.

[13] The stub-end track at Court Street was normally restricted to one streetcar at a time; however, two were commonly allowed during peak periods.

On October 6, 1906, a conductor was crushed to death between two streetcars while preparing his trolley pole for the return trip - the second such accident at the station.

[13][14] On April 18, 1924, the East Boston Tunnel including Scollay Under was converted from low-platform streetcars to high-platform third-rail-powered rapid transit.

Eastern Massachusetts Street Railway service to Brattle Loop ended on January 13, 1935, though some BERy streetcars continued to use it.

Scollay Square station was wholly renovated, and the northbound tunnel was realigned to accommodate the foundation of Boston City Hall.

The stairways to the lower level were relocated, and a fare lobby was built in a low brick structure at the surface.

[12]: 24 In the late 1970s, Mary Beams - an artist at Harvard's Carpenter Center for the Visual Arts - painted 19 murals which were placed along the wall behind the Brattle Loop.

[24] On February 11, 1983, the Green Line E branch was shut down by snow for several days; a Government Center-Lechmere shuttle ran in its stead - the first use of the Brattle Loop in three decades.

[25] In 1990, the state agreed to a number of transit expansion and renovation projects to settle a lawsuit from the Conservation Law Foundation over the environmental impacts of the Big Dig.

[27] 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.

[28] The main construction contract was awarded to Barletta Heavy Division in July 2013, and site preparation began in mid-November 2013.

For the duration of the closure, the B branch was cut back to Park Street (after the reopening of Government Center station, this would later be modified to keeping it at as the terminus permanently for five more years), while the D branch was cut to Park Street at rush hours and North Station at other times.

[33][34] The 1970s Mary Beams murals - made of house paint on plywood - did not meet fire code for installation in the rebuilt station.

[40] Since the loop opened in 1964, Government Center has been a terminus for scheduled service on one or more branches except for the 2014–2016 closure, 1980–1982, and a short period in 1967.

[1][41] Government Center was the northern terminus of the Green Line from August 22 to September 18, 2022; the closure of the northern section allowed for final integration of the Medford Branch, elimination of a speed restriction on the Lechmere Viaduct, demolition of the Government Center Garage, and other work.