The Red Line rail platforms lie underneath Massachusetts Avenue just north of the center of the square.

Many connecting surface transit routes are served by the Harvard bus tunnel, which runs on the west side of the station.

A secondary fare lobby is located above the middle of both platforms, with small brick headhouses on both sides of Massachusetts Avenue at Church Street near Johnston Gate.

[5] Immediately west of the subway platforms is the 1,380-foot (420 m)-long Harvard bus tunnel, used by MBTA buses and formerly trackless trolleys.

[15]: 24  The West End (which was acquired by the Boston Elevated Railway in 1897) rapidly expanded its electric operations, including other lines meeting at Harvard Square.

This three-track tunnel ran southwest under Brattle Street to a maintenance facility known as ”Eliot Shops”; outbound trains could reverse direction at the pocket track or continue to the yard.

[15]: 33 With an eight-minute running time between Harvard Square and Park Street, the Cambridge Subway was fifteen minutes faster than surface streetcars.

The streetcar tunnel served lines to Watertown, Waverley Square, Belmont, Huron Avenue, and Arlington Heights via North Cambridge.

[28][29][30] At that time, the BERy believed that Harvard would be the permanent terminus; the heavy ridership from the north was expected to be handled by extending rapid transit from Lechmere Square.

Trackless trolleys (trolleybuses) began to use the tunnel with the conversion of the Huron Avenue streetcar line (now route 72) on April 2, 1938.

[34]: 113  On September 5, 1958, the Watertown (71) and Waverley (73) lines and the North Cambridge short turns (now route 77A) were replaced with trolleybuses, ending streetcar service through the tunnel.

[35] Original plans had called for the trolleybuses to be replaced by diesel buses at all times, but this was delayed while the MTA investigated methods to ventilate the tunnel.

[39][38][40] Diesel buses equipped with early catalytic mufflers were tested from 1962 to 1964, with the hope of eliminating most surface bus traffic from Harvard Square.

Much of the site was occupied by BERy and West End Street Railway streetcar barns; the area had been used for horsecar facilities since at least 1871.

[34]: 138 The eastern half of the site housed the Eliot Square Shops, used for storage and maintenance of the Cambridge Subway rolling stock.

[52] The Harvard Square power station, which was built for streetcars in 1897, was located adjacent to Eliot Shops across Boylston Street.

[60] In April 1924, the BERy converted the East Boston Tunnel (later the Blue Line) from streetcars to high-platform metro rolling stock.

[61]: 31–32  A small maintenance facility was built underground near Maverick station, but more extensive work was performed at Eliot Shops.

[34]: 138  In October 1958, the MTA sold the east part of Bennett Yard to the city of Cambridge, which used the paved area as public parking.

[15]: 28 Around 1963, John F. Kennedy originally proposed to build his presidential library near Harvard, on the south side of the Charles River.

[64] In June 1964, then-city councilman Alfred Vellucci proposed to instead locate the library on the site of the Bennett and Eliot railyards, on the northern side of the river.

[65] The MTA had begun offering this site for sale the previous year, with Harvard University and several real estate developers developing bids, as the agency planned for a replacement maintenance facility either near South Station or as part of the planned northwestern Red Line extension.

[67] In January 1966, governor John A. Volpe signed a bill allowing the state to purchase the yards from the now-renamed MBTA, and in turn to give the site to the federal government for the library.

[75] A single segment of wall reading BOSTON ELEVATED RAILWAY CO. 1911 remained in the courtyard of the Kennedy School until a 2015-17 expansion project.

[6] The surviving eastern end of the original outbound side platform, built to accommodate passengers alighting at the former terminus, is still visible from passing trains.

The 1945 Coolidge Commission report — the first major transit planning initiative in the region since 1926 — recommended an extension from Harvard to Arlington Heights via East Watertown.

"Harvard/Brattle", a temporary station built of pressure-treated wood, consisted of two island platforms between three tracks in Eliot Yard, just outside the portal.

[86][87][88] The One Brattle Square shopping complex, opened in 1992, was constructed partially on air rights over the south end of the bus tunnel.

[89][90][91] Harvard Square was planned to be the terminus of a spur of the Urban Ring Project, a circumferential bus rapid transit line.

[100][101] Additional closures of the lower busway took place from March 31 to May 2 and June 21 to December 21, 2020, as decreased ridership during the coronavirus pandemic allowed for faster construction.