Like all surface stops on the line, Saint Mary's Street has two side platforms serving two tracks.

With just over 1,500 daily boardings by a 2011 count, Saint Mary's Street is the second-busiest stop on the C branch, behind only Coolidge Corner.

[2][3] The renovation of Saint Mary's Street - part of a $32 million modification of thirteen B, C, and E branch stations - was completed in 2003.

[4][5] In 2007, the MBTA added a wooden mini-high platform on the outbound side, allowing level boarding on older Type 7 LRVs.

[8] In February 2024, the MBTA indicated long-term plans to possibly move the platforms slightly west, with entrances added at Carlton Street.