The modern station opened in May 1975 as part of the Haymarket North Extension, which replaced the Charlestown Elevated; the old terminal was demolished the next year.

[17] In October 1895, the Massachusetts Superior Court issued orders to eliminate remaining grade crossings in Charlestown.

[22][23] The station opened for suburban traffic by June 1901, while the Cambridge Street bridge was completed that July.

In February 1932, with just a few trains a day stopping, the railroad successfully petitioned the Public Utilities Commission to abandon the station entirely.

[26] On April 18, 1958, the Boston and Maine Railroad received permission from the Public Utilities Commission to drastically curtail its suburban commuter service, including abandoning branches, closing stations, and cutting trains.

Among the approved cuts was the closure of all Eastern Division service south of Lynn, including the Saugus Branch plus mainline stations at East Somerville, Everett, Chelsea, and Forbes.

The station was designed as a major transfer point, with many streetcar lines that had formerly gone downtown truncated to Sullivan.

[31]: 21  Lexington and Boston Street Railway cars from as far away as Lowell ran to Sullivan Square until May 4, 1912, when they were redirected to Harvard station.

[32] The 1912-built upper-level streetcar loop was demolished and rebuilt beginning on October 13, 1946, to handle new trackless trolleys.

By June 1975, some local officials and preservationists sought to preserve and renovate the old elevated station for commercial or recreational use.

[39] The Haymarket North Extension was constructed in the early 1970s along the Haverhill Line right-of-way, with a relocated new Sullivan Square station under the elevated I-93 expressway.

[42][43][44] In 2002, as part of its public art program, the MBTA added panels with artworks by local schoolchildren at Sullivan Square and Malden Center.

[47] A 2018–2019 construction project, funded as part of environmental mitigation of the new Encore Boston Harbor casino, reconfigured Sullivan Square roadways and the station busways.

[50][51] The entire Orange Line, including Sullivan Square station, was closed from August 19 to September 18, 2022, during maintenance work.

[53] Under draft plans released in 2008, Urban Ring buses would have used the existing bus loop, and a new platform would be built to serve the Haverhill and Newburyport/Rockport commuter rail lines.

[54] The project was cancelled in 2010[55] In March 2024, the MBTA announced plans to extend to Silver Line route SL3 from Chelsea to Sullivan via Everett Square.

[56][57] A $10.5 million design contract for accessibility improvements at Arlington, North Station, and Sullivan Square was awarded in April 2020.