[13] The route is supplemented by two daily bus round trips operated by Vermont Translines between Albany and Burlington which act as Amtrak Thruway connections to Empire Corridor trains at Albany–Rensselaer.

The Central Vermont Railway continued to operate the Montrealer, providing passenger service to the eastern and northern parts of the state, until 1966.

Then-governor Howard Dean created the Vermont Rail Council headed by McCormack in 1991, with instruction to study Rutland service, but most attention was focused on the Montrealer.

[22] The state agreed to a $200,000 annual subsidy, which reflected the cost of extending one Empire Service round trip from Albany to Rutland.

[23][24] The Ethan Allen Express began with stops in Rutland, Fort Edward, Saratoga Springs, Schenectady, Albany–Rensselaer, Hudson, Rhinecliff, Poughkeepsie, Croton, Yonkers and New York City.

[25] Because the Adirondack already served the section between New York City and Whitehall, the Ethan Allen Express only added 44 route miles (71 km) and one station (Rutland) to the Amtrak system.

[18][27] The Ethan Allen Express was intended to support tourism in the Rutland areas, particularly winter travel to Killington Ski Resort and Pico Mountain.

[33][34] From August 16 to October 31, 1999, the Vermont Railway operated the Ethan Allen Connection between Rutland and Burlington with an intermediate stop at Middlebury.

[26][37] A baggage car was added to the train for bikes and ski equipment in late 1998, but it could not be used for luggage until February 2000 when an attendant was hired for Rutland station.

[26][48] In October 2008, the Vermont Agency of Transportation (VTrans) proposed eliminating the Ethan Allen Express and replacing it with a bus, citing budgetary restrictions.

In February 2011, VTrans began an investigation into the Vermont Rail System's handling of the Ethan Allen Express after Amtrak ranked VRS as the worst host railroad in the country.

[55] Vermont Rail Systems began track work in April 2011, which reduced travel times by 10 minutes by that October.

The project, funded by both the railroad and the state of New York at a cost of $3.25 million, involved rebuilding about 8 miles (13 km) of track and eight grade crossings.

[57] The Friday northbound trip operated on the same mid-afternoon schedule from July 10 to September 5, 2017, during track work at New York Penn Station.

[26][58] From May 26 to September 3, 2018, the Ethan Allen Express and other Empire Corridor trains were diverted to Grand Central Terminal during further Penn Station track work.

[26][59] On March 26, 2020, the Ethan Allen Express was suspended north of Albany–Rensselaer at the request of Vermont Governor Phil Scott due to the COVID-19 pandemic.

[21][64] In 2005, Senator Jim Jeffords obtained a $30 million earmark for upgrades to the Rutland–Burlington rail corridor in preparation for a possible Ethan Allen Express extension.

[64][65] The Vermont Agency of Transportation (VTrans) applied three times for American Recovery and Reinvestment Act of 2009 funds to rebuild the tracks between Rutland and Burlington; none of the applications were successful.

[69] A separately-funded project constructed a rail tunnel in downtown Middlebury to replace aging bridges and increase clearances for freight use.

[70] VTrans originally planned for trains to lay over overnight at Union Station, but nearby residents objected to having the locomotive idle there.

[70][72][73] In October 2021, Amtrak and Vermont Rail System began running qualification trips between Rutland and Burlington to familiarize train crews with the new route.

[74] Revenue service to Burlington began on July 29, 2022, with trains departing early afternoon northbound and late morning southbound all days.

[80]: 17–19  VTrans also analyzed a possible 7.8 mi (12.6 km) extension of the Ethan Allen Express from Burlington to Essex Junction via the New England Central Railroad Winooski Branch, where transfer could be made with the Vermonter.

[80]: 15–17 In 2014, VTrans and the New York State Department of Transportation studied the potential serving southwestern Vermont either with a second daily train or rerouting the Ethan Allen Express.

[80]: 8–10 In December 2023, the Federal Railroad Administration accepted an application by VTrans to enter the New York–Albany–Mechanicville–Bennington–Rutland–Burlington route into its Corridor Identification and Development Program.