Trains on the line provide frequent daily service along the 460-mile (740 km) Empire Corridor between New York City and Niagara Falls via Albany, the state capital.

[5] The corridor is served by four additional Amtrak trains each day:[5] Downstate, in the Hudson Valley, the portion of the route from Poughkeepsie southward is shared with the Metro-North Railroad's Hudson Line, and sees frequent commuter service, with connections to the Empire Service at Poughkeepsie, Croton-Harmon, and Yonkers.

Today's Empire Service is the descendant of numerous routes dating to 1869, when Cornelius Vanderbilt merged his Hudson River Railroad (forerunner of today's Metro-North Hudson Line) with the New York Central Railroad (NYC), thus linking New York City with Albany.

Marketing emphasized convenient service within the state, with a reduced emphasis on long-distance trains which continued west of Buffalo.

[8] Westward service resumed briefly after May with the introduction of the Chicago–New York City Lake Shore, but this train was canceled on January 6, 1972.

[9][10] Despite doubts about Amtrak's potential success, the company was key in reestablishing some discontinued services along the Empire Corridor.

Service was restored permanently on the old Water Level Route with the reintroduction of the old New York Central train, the Lake Shore Limited, on October 31, 1975.

Prior to that change, all passenger trains from Albany and beyond originated and terminated at Grand Central Terminal, forcing passengers traveling to the Northeast Corridor to transfer via shuttle bus, taxicab, or via the New York City Subway to reach Penn Station.

Since 2012, Amtrak has effectively had operational control over the Hudson Subdivision, handling all maintenance and capital responsibilities.

[15] From July 10 through September 1, 2017, six Empire Service trains (three round trips) used Grand Central Terminal as part of Amtrak's work to make repairs at Penn Station.

In May 2018, the Massachusetts Senate approved funds for a two-year pilot of the "Berkshire Flyer", a seasonal extension of a weekend Empire Service round trip to Pittsfield.

[20] The trial was scheduled to begin in June 2020, but was delayed due to the COVID-19 pandemic and outstanding questions around the program's legal sponsorship.

[25] Service was reduced to eight round trips on November 10, 2024, due to construction work in the East River Tunnels limiting capacity at Penn Station.

[29] Between New York City and Albany–Rensselaer, trains are pulled by a GE Genesis P32AC-DM dual-mode diesel locomotive at speeds up to 110 mph (177 km/h).

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

The need for high-speed rail service has been addressed by former Governor George Pataki, former Senate Majority Leader Joseph Bruno, and members of the New York State Assembly who represent the upstate regions.