The Fairmount Line is a newer MBTA Commuter Rail and not one of the historical lines that have received continuous service since the 1800s. The line is basically a deviation/branch of the Northeast Corridor from Reedville to South Station. The line first saw all passenger service discontinued in 1944 as all service from the now Franklin/Foxboro Line was rerouted onto the Northeast Corridor mainline. The line was almost entirely fully grade separated in the 1920s with one grade-crossing on Bird Street in Dorchester finally closed in the late 1970s.

The MBTA purchased the now freight-only line from Penn Central in 1973 and modernized the line with all Amtrak, Attleborough Line and Franklin Line Commuter Rail service diverted to the Fairmount Line on November 3, 1979. This included simple station platforms that were opened at three stations to service intermediate riders. This was done to allow the full rebuilding of the Northeast Corridor along the Southwest Corridor. Service on the line to these intermediate stations were supposed to be temporary with the stations to close for regular service with the opening of the Southwest Corridor on October 5, 1987.

Service to the intermediate stops was planned to be discontinued with the opening of the new Southwest Corridor, although the local community wanted continued service on the Fairmount Line and the Fairmont Shuttle began operating between South Station and Readville in 1987.

In the 2010s the line was modernized to act more like a rapid transit line than a Commuter Rail Line. The line (except for Readville) was changed to be fully in Zone 1A, where a one-way Commuter Rail trip is the same as a Subway fare – although no free transfers – with free rides for passengers with 1 Day, 7 Day and Monthly Link Passes. As part of these plans three new stations were opened in 2012, with five more round-trips added. Weekend service finally began on the line in 2014.

In the early 2020s service on the line was improved even more. Service was gradually increased with 30 minute frequencies added to the line (including on weekends) on May 20, 2024. This included all weekend Franklin/Foxboro Line trains now rerouted over the Franklin Line. Carlie Card Readers were added to all stations in 2020, allowing passengers to tap their CarlieCards to ride this line the same as a regular subway line, including free transfers to Subways and Buses for all passengers using the new Rapid Transit Line-like Commuter Rail Route.