In 1959 the section from Reading to Wilmington Junction became freight-only, and Haverhill commuter trains as well as intercity service from New Hampshire and Maine were rerouted over the Wildcat Branch and the lower Lowell Line.

[3] However, local opposition to the extension - largely in Melrose, where rapid transit conversion would have required the elimination of grade crossings, possibly blocking important east-west local roads - and funding issues meant that the Orange Line only reached Oak Grove.

On April 7, 1975, town residents voted "overwhelmingly" to reimburse the commuters and subsidize service for an additional year.

[3] The MBTA bought all B&M commuter equipment and lines on December 27, 1976, including the Western Route from Wilmington Junction to the New Hampshire border.

Weekday service was restored to Haverhill via Reading with funding from the Merrimack Valley Regional Transit Authority on December 17, 1979.

[3] The switch may have been made due to a request by John A. Brennan Jr., who was then constructing a large development near Malden Center station.

[3] The Downeaster runs via the lower Lowell Line and the Wildcat Branch then the Western Route, with a stop at Haverhill.

[9] In early 2009, the MBTA began planning the addition of double track between Reading and Ballardvale that summer.

[14] By late 2013, a 1,300 feet (400 m) stone wall at Andover station had been replaced, along with a century-old culvert, as part of drainage improvements.

[17] In 2011, the Northern New England Passenger Rail Authority won a $20.8 million federal grant to add additional double track from Wilmington Junction to just south of Ballardvale station.

A temporary one-track wooden trestle was constructed to the west of the bridge; the truss spans were jacked up 2 feet (0.61 m) at a time while the masonry piers were built up under them.

[31] Repairs were also made to two smaller arch bridges over the Shawsheen River in Andover, both dating to the line's opening in 1839.

The MBTA constructed a two-track layover yard adjacent to a rebuilt Bradford station at a cost of $2.2 million.

[33] Because of its proximity to the Bradford residential neighborhood, the noise and diesel fumes from the layover have prompted continued complaint from residents.

[41][42][43] However, the Plaistow Board of Selectmen voted for the "no build" option to not extend commuter rail to the town in April 2015.

[45] The line was shut down on weekends in September through December 2017 for the installation of Positive Train Control equipment in order to meet a 2020 federal deadline.

[47] Continuous welded rail was installed on an 11.5-mile (18.5 km) section between Fells Interlocking in Malden and the Ipswich River in Wilmington from September to November 2021.

Most off-peak service between Reading and North Station was cancelled, with many Haverhill trains operating using the Wildcat Branch.

[52] From May 20 to September 29, 2024, weekday midday inbound trains were temporarily routed over the Wildcat Branch during rail replacement work.

[53][54][55] In 2024, the town of North Andover began a planning study for a potential infill station at the Osgood Landing development.

[56] Replacement of the South Elm Street bridge in Bradford caused Haverhill station to be closed for MBTA service on July 15, 2024.

[60][61] Mileages to the New Hampshire stations are via the Wildcat Branch and Wilmington – 0.4 miles (0.64 km) longer than the mainline through Reading – which was the route used at the time of discontinuance.