Service resumed in 1989 after Amtrak seized control of the line in Vermont from the Boston and Maine Railroad, but the train was rerouted over the Central Vermont Railway through Massachusetts and Connecticut to avoid the still-dilapidated Connecticut River Line, because Guilford Rail System refused to improve poor track conditions.

The Montrealer was replaced by the daytime Vermonter in 1995, using the original route through Connecticut but still avoiding the Conn River Line in Massachusetts.

In recent years the line has been operated at FRA Class I levels, with freight trains limited to a maximum speed of 10 miles per hour (16 km/h).

One of the largest potential customers, Yankee Candle, despite being on the other side of the road, receives wax shipments via truck from a competing railroad's depot further south.

[15] A 2014 state transportation funding bill included $30 million for acquiring used MBTA Commuter Rail rolling stock and new locomotives for the service.

[17] In 2014, following several years of planning and construction, the original mainline was restored to modern standards, with a maximum authorized speed of 79 miles per hour (127 km/h) for passenger trains on the long straight sections of track between Hatfield and Deerfield.

In February 2016, Massachusetts Secretary of Transportation Stephanie Pollack said that MassDOT was looking at starting a pilot commuter service as early as 2017.

[19] In June 2018, Governor Charlie Baker announced that two Amtrak Shuttle round trips would be extended to Greenfield in 2019 as a pilot program.

In October 2022, MassDOT and Amtrak announced that the Valley Flyer service had matched projected ridership and would be made permanent.