In 1989, a group of volunteers founded TrainRiders/Northeast, a non-profit organization dedicated to bringing modern passenger rail service to Northern New England.

In 1995, Governor Angus King and Commissioner of Transportation John Melrose ordered the creation of a passenger rail authority.

TrainRiders/Northeast, led by Chairman Wayne Davis,[5] worked with the state Chamber of Commerce and industry, Maine DOT, and others to convince the legislature to create the Northern New England Passenger Rail Authority in August.

Most right-of-way improvements were complete in 2000, but the following year, start-up was delayed again when Guilford refused to allow Amtrak to test track modulus or run trains faster than 59 miles per hour (95 km/h).

The first expansion of Downeaster service came that month, when the improvements made it possible to increase from four to five daily round trips from Portland to Boston.

A new location could put the station on the main line, move it closer to downtown, and improve vehicular and pedestrian access.

[20] In October 2000, the Federal Railroad Administration designated a route from Boston to Portland and Auburn as one component of the Northern New England Corridor, a proposed high-speed rail project.

[21] Service to Brunswick was originally intended to begin within five years of the Downeaster's 2001 launch, but was delayed by lack of funding and other obstacles.

Ground was broken in October 2008 for the Brunswick Maine Street Station, a retail development that included shops, condominiums, an inn, and office space.

In January 2010, NNEPRA received a $35 million grant from the American Recovery and Reinvestment Act of 2009 for track and signal upgrades for the Portland-Brunswick line.

[24] The extension to Brunswick led to the construction of an enclosed layover facility there, just west of the station; trains had previously been stored outdoors in Portland.

[8][25] NNEPRA announced plans for the facility in 2013, with construction slated to run from summer 2013 until late 2014,[26] but local opposition delayed the project.

[28] Several Democratic state legislators asked NNEPRA to build in an existing rail yard in South Portland, and to focus on the "core product" of Boston-Portland service instead.

[34] The Downeaster's ridership, finances, and performance suffered in the first half of 2015 because of an exceptionally brutal winter and a subsequent large-scale tie replacement project funded by the NNEPRA.

[39] On June 24–27, 2021, Downeaster trains stopped at Falmouth Country Club to serve attendees of the Live and Work in Maine Open.

[40] Design work for positive train control (PTC) over the section of the route between Haverhill and Brunswick was completed in March 2023.

[44] All classes of service include complimentary WiFi, an electric outlet (120 V, 60 Hz AC) at each seat, reading lamps, fold-out tray tables.

[45] Some Downeaster trains carry volunteers, coordinated by Trainriders Northeast, to inform passengers about destinations, attractions, and transfers.

[55] A 2008 study by the Chicago-based Center for Neighborhood Technology suggested that the Brunswick extension, combined with commercial developments along the "Downeaster Corridor", could generate several billion dollars in construction investments plus $55 million annually in tax revenue for the state of Maine.

[56] In 2013, the Northern New England Passenger Rail Authority estimated that the Downeaster has an annual economic impact of $12 million from visitors to Maine, and directly or indirectly employs 200 people.

Senator Ed Markey,[60] former Massachusetts governor Michael Dukakis, and others who are pushing for the connection so the diesel engines that currently haul the Downeaster can be replaced by electrified ones.

In April 2015, Representative Michelle Dunphy and nine cosponsors introduced a bill in the Maine House that would direct MaineDOT to study the feasibility and cost of extending passenger rail to Bangor.

Some politicians, including Baldacci and Auburn mayor Jason Levesque, stated that they would continue to pursue a rail extension.

An August 2011 feasibility study by MaineDOT examined a Portland-to-Auburn service, which would take 40 minutes and consist of eight daily round trips.

From 2003 to 2015, the Maine Eastern Railroad leased operation of the line, offering seasonal excursion service to Rockland.

[82][83] The proposed pilot was later pared to three weekends in summer 2018, before ultimately being cancelled when Amtrak failed to conduct a risk assessment in time.

[84] Plans for a summer 2019 pilot also fell through when time ran out to reach a contract with the Central Maine and Quebec Railway.

[85] In August 2019, local stakeholders inspected the route aboard an Amtrak track geometry car, looking toward a summer 2020 pilot.

[89] Amtrak's map lists stops in Waldoboro and Thomaston, as well as those previously proposed in Bath, Wiscasset, and Newcastle.

[17] The rail shuttle would connect Commercial Street in Portland with high-density developments at Thompson's Point, Rock Row, and to other transit services, which would support private investments and reduce the growing congestion.