The Main Line was rerouted into the Washington Street tunnel, with Union and Friend stations at Haymarket Square, in 1908.

The Green Line entrance is located north of Sudbury Street, under the east end of the Government Center Garage.

The Orange Line entrance is inside the Boston Public Market building south of Sudbury Street.

Haymarket is a major bus transfer station, with a (presently closed) two-lane busway off Surface Road adjacent to the Green Line headhouse.

[3] Haymarket is also the terminus for several early-morning round trips, which are extensions of routes that normally terminate at subway stations outside downtown.

[4] The Tremont Street subway (future Green Line), including Haymarket, was built starting in 1894 and opened on September 3, 1898.

The inner pair of tracks served cars from the northern suburbs which turned at Brattle Loop at Scollay Square (now Government Center) station, while the outer tracks served streetcars that ran through the entire Tremont Street subway to the Public Gardens portal and Pleasant Street portal.

The Tremont Street subway was retrofitted to allow operation of the Main Line elevated cars.

[4] On May 10, 1971, the MBTA opened a new Green Line platform at Haymarket, located south (inbound) of the 1898-built station.

[5] In August 1975, the MBTA released plans to modernize four downtown stations, including the Orange Line platforms at Haymarket.

[4] In June 2004, the Green Line was similarly rerouted, with the Canal Street incline closing entirely in favor of a tunnel to a newly rebuilt "superstation" at North Station.

[7] A $15 million project to build raised platforms at Park Street and Haymarket began in 2001 and was completed by 2003.

[11] Much of the cosmetic work at Haymarket, including painting and floor repairs, was completed over the weekend of August 30–September 1, 2019.

[25] After removal of about 100 short tons (91 t) of debris followed by tunnel inspection and testing, Green Line service resumed on April 9, with Haymarket station remaining closed for repairs to the standpipe system.

[28] The Orange and Green lines were again closed through Haymarket from June 23–26, 2022, after the discovery of a deteriorated garage support column.