Jabarkan Expansions dari MBTA Commuter Rail

The late 1980s saw the beginning of substantial expansion of the system. The Southwest Corridor project was completed in 1987 with a new below-ground alignment for commuter rail, Amtrak, and Orange Line trains. Back Bay and  stations were completely rebuilt as transfer stations, and  opened to serve the growing Longwood Medical Area. The Needham Line, closed since 1979 for construction, was reopened. The Attleboro and Franklin lines had been diverted over the previously freight-only Dorchester Branch during construction; after they returned to the Southwest Corridor, a shuttle service was retained as the Fairmount Line. Peak-hour service to Providence resumed in 1988 (with off-peak and weekend service later added);  was added in 1990 as a park-and-ride station to replace . The Franklin Line was extended to  in 1988; infill stations in that era included  in 1988 to serve Boston Red Sox games at Fenway Park, and  in 1990.

Massachusetts had state accessibility laws since 1977 – prior to 1990 federal legislation. At times, the MBTA clashed with state regulators: several stations including West Natick and Chelsea were built without accessible platforms despite state rules; the latter resulted in fines from the Massachusetts Architectural Access Board (MAAB). The opening of South Attleboro was delayed by the MAAB because of the MBTA's refusal to build full-length high-level platforms. However, the MBTA did slowly increase accessibility of the system. Most Ipswich/Rockport line stations were made accessible during the 1984–85 closure, and renovations followed at other stations. South Station was made accessible in the late 1980s, Back Bay during the Southwest Corridor project, and North Station in the early 1990s, providing accessibility at the main downtown Boston stations. By 1992, 44 commuter rail stations were accessible.

In 1991, the state agreed to build a set of transit projects as part of the settlement of a lawsuit by the Conservation Law Foundation (CLF) over auto emissions from the Central Artery/Tunnel Project (Big Dig). Among these project were extensions of the Framingham Line to Worcester and the Ipswich/Rockport Line to Newburyport, restoration of the Old Colony Lines, and addition of 20,000 park and ride spaces outside the urban core. Peak-hour service to Worcester began in 1994, followed by off-peak and weekend service; four intermediate stations were added in 2000 and 2002. Service on the Old Colony Lines (Middleborough/Lakeville Line and Kingston/Plymouth Line) began in 1997.  and  opened in 1998. The MBTA Commuter Rail Maintenance Facility, which replaced the ex-B&M Boston Engine Terminal, was completed in 1998.

Two tenders were submitted in 2003, one from GTI and another from the newly formed Massachusetts Bay Commuter Railroad Company (MBCR), a partnership between Connex (later Veolia), Bombardier Transportation and Alternate Concepts, Inc. MBCR won the contract, and took over the MBTA Commuter Rail operation from Amtrak in July 2003. The MBCR contract originally expired in July 2008 but had an additional five-year option; it was later extended three years to July 2011 and then another two to July 2013. After concerns about on-time performance, the 2011 extension increased the fine for late trains from $100 to $300.

The MBTA considered running the service directly rather than contracting it out, but this "public option" was rejected in 2012. In August 2012, MBCR and Keolis were the two bidders for the contract. On January 8, 2014, the MBTA awarded Keolis the contract for $2.68 billion over eight years, with the possibility of two two-year extensions that could bring the total price to $4.3 billion. Keolis took over the operations on July 1, 2014. Keolis lost $29.3 million in its first year of operation. In June 2020, the MBTA extended the contract through at least 2025.

Free Wi-Fi internet service was piloted in January 2008 on the Worcester Line, where 45 coaches were fitted with routers which connected to cellular data networks. This was the first Wi-Fi available on a commuter rail service in the United States. The program was considered successful; in December 2008, the MBTA announced that Wi-Fi would be available on all trains by mid-2009. In July 2014, the MBTA announced that a private company would be building a new network by 2016 to replace the 2008-built network. The MBTA would not pay for the new network; the company would have a two-tier model with a fee for higher bandwidth. The MBTA canceled the plan in August 2017 due to local opposition to the erection of 320 monopoles, each  tall, as well as the need to focus on more critical projects like the Green Line Extension. By that time, the 2008-built system was largely unusable to the decommissioning of 3G networks.

Positive Train Control was implemented on the entire system per a federal mandate, which required installation by the end of 2018 with the possibility of a two-year extension. Construction began in 2017. The final segment of the system to have Positive Train Control activated was the inner Worcester Line on August 15, 2020. Most of the southside lines already had cab signals for automatic train control (ATC) prior to PTC implementation, but the northside lines did not. Cab signals on the southside were completed in 2020; cab signals on the northside will be completed in 2023. Temporary bus replacements for several lines took place between 2017 and 2022 during PTC and ATC construction and testing.

The Greenbush Line opened in 2007.

The Riverside-Framingham section was sold to the MBTA in 1976 as part of their larger acquisition of PC commuter assets, but the section past Framingham remained in Conrail control. In September 2009, Conrail successor CSX Transportation and the Commonwealth finalized a  agreement to purchase CSX's Framingham to Worcester tracks, as well as the Grand Junction Railroad plus lines which will be part of the South Coast Rail project, to improve service on the Framingham/Worcester Line. After several years of construction and negotiations, ownership of the line was transferred to the commonwealth on October 4, 2012, with increased service on the outer section of the line beginning several weeks later.

As Big Dig mitigation, MBTA rebuilt existing stations and is adding 4 new stations along the line. The first of these, Talbot Avenue, opened on November 12, 2012, followed by Newmarket and Four Corners/Geneva on July 1, 2013. Blue Hill Avenue station was opened on February 25, 2019, after many delays.

Service was extended further south to  T. F. Green Airport in Warwick, Rhode Island in December 2010 and to Wickford Junction in North Kingston in April 2012. This represents the first commuter service in Rhode Island south of Providence since 1981.

In 2013, the CapeFLYER service began running from South Station to Hyannis on summer weekends – the first direct service from Boston to Cape Cod since 1959. Though officially a Cape Cod Regional Transit Authority service, the CapeFLYER uses MBTA equipment.

A 4-mile extension of the Fitchburg Line to Wachusett station opened on September 30, 2016.