The station was opened February 16, 1941 as part of the Huntington Avenue tunnel, which was a WPA project that eliminated street cars from Boylston Street and Copley Square in order to ease congestion. The trolley cars emerge onto the street immediately south of Symphony station. There is a sub-passageway connecting the inbound and outbound platforms that was sealed off in the early 1960s when the MTA converted the station to an unmanned one, as it is today. Moderate renovations were performed to the station in the early 1990s which included new tiling and improved lighting.
Formerly, Symphony and Prudential were the only two underground stops on the Green Line where riders paid boarding the train rather than when entering the station. This changed in May 2006 when the MBTA installed the Charlie Card / Charlie Ticket electronic fare collection system at the station. Passengers now pay with their Charlie Card/Ticket when entering the station, and can board at any door to the train.