The tubes originate at a junction of two PATH lines on the New Jersey shore and cross eastward under the Hudson River.

In 1901, a company formed by William Gibbs McAdoo resumed work on the tubes, and by 1907, the tunnels were fully bored.

After the Uptown Hudson Tubes' opening, the H&M proposed extending them northward to Grand Central Terminal, as well as creating a crosstown spur line that would run under Ninth Street in Manhattan.

As well, they were built when today's Midtown Manhattan was considered "uptown" and the true northernmost reaches of the island were not as densely developed.

[2]: 7  The name "Uptown Hudson Tubes" also applies to the section of the subway under Christopher Street and Sixth Avenue in Manhattan.

[9][13]: 125  Shield tunneling was used only between the Uptown Hudson Tubes' western end in Jersey City and 12th Street in Manhattan.

[18]: 2 [2]: 12 An initial attempt to construct the Hudson River tunnel began in November 1874 from the Jersey City side.

[22] Work had progressed for only one month when it was stopped by a court injunction submitted by the Delaware, Lackawanna and Western Railroad, who owned the property at the tunnel's New Jersey portal.

[18]: 2  As a result of the lawsuit, work on the tunnel was delayed until September 1879, when the judge ruled in favor of the builders and the injunction was dissolved.

Haskin believed the river silt was strong enough to maintain the tunnel's form—with the help of compressed air—until a 2-foot-6-inch-thick (76 cm) brick lining could be constructed.

Haskin's plan was to excavate the tunnel, then fill it with compressed air to expel the water and to hold the iron plate lining in place.

On July 21, 1880, an overpressure blowout at the tube's top caused an accident that resulted in an air lock jam, trapping several workers and killing 20.

[15][18]: 2 In 1888, an unnamed British company attempted to finish the Morton Street Tunnel; it employed James Henry Greathead as a consulting engineer and S. Pearson & Son as principal contractors.

To maintain sufficient air pressure inside, S. Pearson & Son decided to place a silt layer of at least 15 feet (4.6 m) above the tube.

[18]: 4 [22] The bulkhead contained a pressurized air lock in order to avoid sudden blowouts, such as had occurred during the original construction.

[2]: 17 [22] McAdoo later noted that the Uptown Hudson Tubes effort was the first project where machines, rather than workers, carted out the excess silt.

[2]: 17–18 [18]: 4 [31] By the end of 1904, the New York and Jersey Railroad Company had received permission from the New York City Board of Rapid Transit Commissioners to build a new subway line through Midtown Manhattan, which would connect with the Uptown Hudson Tubes; the company received the sole rights to operate this line for a duration of 25 years.

The Rapid Transit Board changed its decision after Sixth Avenue property owners expressed opposition to the rejection.

The company, which was contracted to construct the Uptown Hudson Tubes' subway tunnel connections on each side of the river, had a capital of $21 million to complete the project.

[36][37] The Downtown Hudson Tubes, located about 1.25 miles (2.01 km) south of the first pair, had started construction by that point,[2]: 19  and would ultimately open in July 1909.

[2]: 18 [38][39] Digging for the Uptown Hudson Tubes was completed in 1907, after 33 years of intermittent effort; they were celebrated as the first non-waterborne link between Manhattan and New Jersey.

[48] On July 19, 1909, service via the downtown tubes commenced between Hudson Terminal in Lower Manhattan and Exchange Place in Jersey City.

[52][53] The original plans for the Uptown Hudson Tubes called for a terminal at 33rd Street under the Gimbels department store, now Manhattan Mall.

During construction, the plan was changed so the 33rd Street station was directly under Sixth Avenue, providing for a future northward extension.

[55] As an alternative, the city's Utilities Board proposed connecting the Uptown Hudson Tubes to the Steinway Tunnel.

[56] A franchise to extend the Uptown Hudson Tubes to Grand Central was awarded in June 1909, with the expectation that construction would start within six months and that the extension would be operational by January 1911.

[60] On its seventeenth application, the Rapid Transit Commissioners declined the request for a delay, effectively ending the H&M's right to build an extension to Grand Central.

One of the proposed routes, the Sixth Avenue Line, ran parallel to the Uptown Hudson Tubes from Ninth to 33rd streets.

[61] At first, the city intended to take over the portion of the Uptown Hudson Tubes under Sixth Avenue for IND use, then build a pair of new tunnels for the H&M directly underneath it.

[78] Service on the Uptown Hudson Tubes was suspended for five days in 1962 when it was discovered that builders constructing the express tunnels had drilled to an "unsafe" margin of 18 feet (5.5 m) underneath.