All Amtrak Acela Express and Northeast Regional trains running to and from South Station stop at Back Bay, as does the Boston section of the Lake Shore Limited.

The Dartmouth Street Underpass connects the Copley Place shopping mall with the main station building.

[7] Around 1880, the Boston and Albany Railroad (descendant of the B&W) opened its Columbus Avenue station to serve new developments on the filled bay.

[12] The current Back Bay Station opened on May 4, 1987, as part of the Orange Line's Southwest Corridor project and was dedicated by Governor Michael Dukakis.

[15] The 1987 reconstruction added a waiting area with a 9-foot bronze statue dedicated to civil rights and labor movement pioneer A. Philip Randolph.

The area includes various posters with historical photographs and interview excerpts regarding Randolph's career in organizing the Brotherhood of Sleeping Car Porters and work with the Civil Rights Movement.

[16] On September 22, 2006, the MBTA began allowing free inbound travel from Back Bay to South Station.

[17] Until replaced with the CharlieCard Store at Downtown Crossing on August 13, 2012, an MBTA customer service booth for special pass users was located at Back Bay station.

Much of the commuter rail infrastructure at Back Bay is covered and enclosed, and so diesel fumes cannot escape quickly to the outside air.

An earlier study showed elevated levels of carbon monoxide, formaldehyde, particulates, and oxides of nitrogen, though it noted that there is no regulated standard to meet for indoor air quality in public spaces.

Though simple changes were made regarding scheduling, and checking to make sure train engines were running properly, in 2008 the MBTA claimed it lacked the financial resources to fully upgrade the ventilation system.

[25] On October 8, 2014, Amtrak removed its customer service and ticketing agents from the station due to the persistent air quality issues.

The work will improve ventilation at the platform level and add "air curtains" to prevent exhaust fumes from reaching the concourse.

In August 2015, the MBTA began paying Boston Properties a subsidy (as rents from retail spaces had been lower than expected) and agreed to fund some repairs to expansion joints not covered in the original agreement.