[5] A $150 million project completed in 2017 included adding nine miles of double track, an extension to Wachusett, rebuilding two stations, and building a new layover yard.

Service was restored as far as Ayer on June 28, 1965, along with the outer Rockport Branch and full schedules on the Lowell and Ipswich routes.

[12] Although some gains were made, including the reopening of Belmont Center and Waverley stations on March 4, 1974, the system continued to hang on by thin margins.

[12] On December 27, 1976, the MBTA bought the Boston and Maine Railroad's northside commuter rail assets, including the entire length of the Fitchburg Line.

Due to the cyclic expansion and contraction for the first three decades of the MBTA's existence, the Fitchburg Line was largely neglected and its infrastructure began to decline.

The Fitchburg route was once fully double tracked from Boston to Troy, New York; however, the second main was removed in many sections as passenger service declined.

[5][18] The 2004 edition of the Program for Mass Transportation found that restoration of service all the way to Gardner, much less Athol, was deemed impractical for several reasons.

[8] The line between Fitchburg and Gardner would cost $104.2 million to double track, and speeds are limited due to the grades going through the Wachusett Mountain range.

Because the Route 2 expressway is faster along the corridor than rail service would be, the station at Gardner would have attracted just 50 riders per day.

The Fitchburg Commuter Rail Line Service Expansion Study was released in February 2005, drawing off the PMT conclusions.

[20] The report priced out $55 million in infrastructure upgrades including double tracking through downtown Waltham and from South Acton to Willows, signal improvements, rebuilding Littleton/Route 495 station, and grade crossing modifications.

The MBTA applied for a federal Small Starts grant in September 2005, and the Montachusett Regional Transit Authority filed a scoping package in April 2007 that began the analysis of construction alternatives.

[25] In November 2007, following the completion of five years of conceptual studies, the MBTA announced $150 million in projects to significantly upgrade the Fitchburg Line.

Financed by $10.2 million in ARRA funds, the work was intended to "provide commuter rail operational flexibility and to minimize conflicts with freight".

[30] Originally to be completed in August 2013, the garage was delayed due to high summer heat which prevented pouring concrete as well as contractor's financial problems.

Like many of the outer stations on the line, Littleton/Route 495 was built in 1980 with a bare low-level concrete platform (not accessible for handicapped riders) serving a single track.

[34] The double tracking work, including 8 grade crossing replacements and a new interlocking just east of Littleton station, was completed in November 2014.

After significant design changes based on community input, construction started on a new station with two full-length high-level side platforms in September 2012.

[28] Previously, the section of the line east of Acton had an older signalling system which permitted operations in one direction on each track, which prevented express trains from passing locals and limited schedule density.

The double-tracked section west of Willows, which already had bidirectional signalling to permit passenger and slower freight trains to mix, received incremental upgrades.

[27] Thirteen grade crossings were replaced, nine interlockings built new or improved, and dispatching of some segments transferred from the outdated tower at Waltham to the MBTA's control center.

[27] Per the recommendations of the mid-2000s studies, the line was extended 4.5 miles (7.2 km) west of Fitchburg to a new Wachusett park-and-ride station.

[38] Construction was eventually allowed to proceed; the layover yard opened on November 21, 2016, along with full service to Wachusett station.

[12][27] Work like laying track, connecting switches, and testing new signals was difficult or impossible to perform during regular daily service.

[12] In November 2020, as part of service cuts during the pandemic, the MBTA proposed to close Hastings, Silver Hill, and four other low-ridership stations on other lines.

[12][42] That day, the MBTA Board voted to enact a more limited set of cuts, including indefinitely closing Hastings, Silver Hill, and three of the other four stations.

[53][54][55] Additional weekday short turn service was operated between Porter and North Station from July 15–26, 2024, providing half-hour headways between those points while the Red Line was closed for maintenance work.

[58] The MBTA has unsuccessfully attempted to sell air rights for development over the tracks along Somerville Ave, near Porter station.