Boylston has a peculiar layout. Four tracks run between it and Park Street, but they have different levels of use. The two inner tracks are still in regular use, but the outer ones are not, and their platforms have been fenced off. Track 1 is used to store MOW equipment, while Track 4 has a display track with a pair of trolleys from Seashore Trolley Museum on it. The rights-of-way for both outer tracks continue south to the abandoned Pleasant Street portal, with Track 1 diving below the two in-service tracks, which make a sharp turn west just south of the station to go into the Boylston Street Subway (opened in 1914. Originally, the tracks went to the Public Garden Incline, which is long gone).

The outbound platform is north of the inbound platform, with the inner tracks shifting over a few yards in between. There used to be a passageway below the tracks that connected the two platforms, but that was sealed up decades ago to keep the homeless out of it.