The Indigo Line was a proposed urban rail transit service of the Massachusetts Bay Transportation Authority (MBTA) that would have incorporated parts of the former Grand Junction Railroad, the Seaport District's Track 61, a spur to Riverside station and segments of other MBTA Commuter Rail lines within the Greater Boston region of Massachusetts. As proposed, the Indigo Line would have predominately shared existing infrastructure with the MBTA Commuter Rail.

The Indigo Line was formally endorsed in 2014 during the Deval Patrick administration. The service was included within the Massachusetts Department of Transportation's (MassDOT's) 2014-2018 Capital Investment Plan which consolidated recommendations put forth by the Boston Redevelopment Authority (now the Boston Planning and Development Agency) and several other proposals by community advocates. The MBTA planned to procure diesel multiple units (DMUs) for Indigo Line service with full-build completion projected for 2024.

Despite initial planning efforts, the project faced financial, political, and logistical hurdles. The Baker administration blocked funding for the Indigo Line in 2015, with the project being officially canceled by the MBTA shortly after. In the years following the project's cancelation, lawmakers and local advocates have called for the revival and reassessment of the Indigo Line plan in relation to improvements to the MBTA Commuter Rail's Fairmount Line. Several minor projects based on preliminary Indigo Line recommendations have been pursued; however, the Indigo Line project as originally proposed has been abandoned.

Conversion of underutilized rail infrastructure within the Greater Boston area into regional rail or light rail services has been discussed for several decades, mostly about the Fairmount Line. The MBTA has traditionally extended rapid transit lines adjacent to existing suburban railroad rights-of-way to provide increased frequencies within Greater Boston (as with the Green Line Extension, Red Line Braintree Extension, and the Haymarket North Extension). In the case of the Green Line D Branch, a commuter line (the Highland Branch) was fully converted into a streetcar rapid transit line. The Indigo Line proposal was intended to make the characteristics of existing commuter lines more like rapid transit than commuter rail, with increased frequency and number of stops through the use of DMUs (which operate as self-propelled railcars without the need for an auxiliary electrification system) without incurring the costs associated with extending subway or light rail lines.

Prior to the formal endorsement of the Indigo Line, several planning initiatives during the 2000s would serve as the basis for the DMU proposal. Part of the environmental mitigation negotiated by the Conservation Law Foundation (CLF) for the Big Dig was improved commuter rail service on the Fairmount Line; following advocacy for the Fairmount Corridor Coalition (later the Fairmount Indigo Transit Coalition) in 1999-2000, the MBTA pledged half of the money necessary to build additional stations along the Fairmount Line in 2002. The remaining necessary funds were put into the MassDOT budget in 2005-06 following a lawsuit by the CLF for inadequate completion of Big Dig mitigation measures. The existing Uphams Corner and Morton Street stations were rebuilt, and four new stations were constructed at Four Corners/Geneva, Talbot Avenue, Blue Hill Avenue, and Newmarket in the 2010s; however, no plans were included to increase service on the line. While plans for the station improvement projects moved forward, community advocates would call for the conversion of the Fairmount Line to rapid transit.

Early plans to establish rapid DMU service within Boston stems from early Urban Ring planning within the Allston Multimodal Station Study (what would later become the West Station proposal) in 2007. The study analyzed both commuter rail and DMU local service along the Framingham/Worcester Line corridor, with potential stops at Faneuil, Market Street, Everett Street, Cambridge Street, West (Ashford Street), and Commonwealth Avenue. The final recommendation called for a commuter rail station at Everett Street with DMU stops added later at the other locations.

The term "Indigo Line" dates back to The Fairmount/Indigo Corridor Collaborative (FCC) community campaign in 2004 which advocated for expanded service on the Fairmount Line; however, official development of the proposal would be established with the creation of the Fairmount Indigo Planning Initiative in 2012. This study was facilitated by the Boston Redevelopment Authority which recommended transforming the Fairmount Line into a hybrid rail service. Hybrid rail, which emerged during the early 2000s with systems such as New Jersey Transit's River Line, was intended to be a low cost alternative to implementing high-frequency services on existing right-of-ways through the use of FRA non-compliant DMUs. The Indigo Line concept would be further consolidated with other DMU proposals with the intent to upgrade several other lines beyond the Fairmount Line. The "Indigo" terminology for the service was intended to denote it within Boston's rapid transit network, which utilizes a color-labeled nomenclature, since it would be operationally separate from the purple-denoted MBTA Commuter Rail network.

In 2014, the Indigo Line was formally endorsed by Governor Deval Patrick. The project was included as a capital project within MassDOT's annual five-year capital plan; however, no capital funding was allocated. The proposal was further outlined within the "MBTA Vision for 2024" proposal that same year. Within the Vision for 2024 plan, the MBTA reciprocated the recommendation to operate Indigo Line services as hybrid rail, with Fairmount Line DMU service being fully operational that year with leased equipment. The full buildout of the Indigo Line network was projected for completion by 2024 at a total capital cost of $252 million.